Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/inputs/xco Working: n-1-21.cluster.ucsf.bkslab.org:/scratch/xiaobo/281161/xco-8058088.67 Result: /scratch/xiaobo/281161/xco-8058088.67 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco 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/xco mkdir: created directory `/scratch/xiaobo/281161' mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67' /scratch/xiaobo/281161/xco-8058088.67 /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/281161/xco-8058088.67/working' mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/protonate' Storing results in /scratch/xiaobo/281161/xco-8058088.67/finished Working in /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 /scratch/xiaobo/281161/xco-8058088.67/working/protonate /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Using inputs as protomers/tautomers. No processing done 472 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/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Bulk generating 3D conformations all protomers in /scratch/xiaobo/281161/xco-8058088.67/working/3D mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/281161/xco-8058088.67/working/protonate/xco-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' 999 3D conformations generated for 1000 compounds Building ZINC000302998030 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building' mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998030' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC000302998030 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998030/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/1 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/1' -> `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(C(=O)N2CCCC[C@@H]2C)c(Cl)c1) `ZINC000302998030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302998030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000302998030 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 16, 16, 16, 28, 28, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 16, 16, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000302998030 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/finished' Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998030/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998030 Building ZINC000302998031 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000302998031 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/2 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/2' -> `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(C(=O)N2CCCC[C@H]2C)c(Cl)c1) `ZINC000302998031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302998031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000302998031 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 29, 29, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/3 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/3' -> `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(C(=O)N2CCCC[C@H]2C)c(Cl)c1) `ZINC000302998031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302998031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000302998031 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 16, 16, 16, 29, 29, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 92 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000302998031 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 Building ZINC000302998031 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000302998031 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 2) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/2: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)c(Cl)c1) `ZINC000302998031.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000302998031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000302998031 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 16, 16, 16, 29, 29, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 3) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)c(Cl)c1) `ZINC000302998031.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000302998031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000302998031 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 16, 16, 16, 29, 29, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 92 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000302998031 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000302998031 Building ZINC000303065824 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303065824 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/4 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)O[C@@H](C)C1) `ZINC000303065824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303065824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065824 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)O[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 4, 7, 7, 7, 7, 10, 10, 8, 10, 10, 7, 7, 7, 7, 7, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 7, 7, 10, 10, 10, 10, 10, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/5 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/5' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)O[C@@H](C)C1) `ZINC000303065824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303065824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065824 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)O[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 30, 30, 4, 30, 30, 30, 30, 30, 30, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 4, 4, 4, 30, 30, 9, 30, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 90 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303065824 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 Building ZINC000303065824 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303065824 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 4) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)O[C@@H](C)C1) `ZINC000303065824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303065824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065824 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)O[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 4, 4, 7, 7, 7, 7, 10, 10, 8, 10, 10, 7, 7, 7, 7, 7, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2, 7, 7, 10, 10, 10, 10, 10, 7, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 77 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 5) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)O[C@@H](C)C1) `ZINC000303065824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303065824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065824 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](c2ccccc2)O[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 12, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 30, 30, 4, 30, 30, 30, 30, 30, 30, 4, 4, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 4, 4, 4, 30, 30, 9, 30, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 90 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303065824 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065824 Building ZINC000303065825 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303065825 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/6 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1) `ZINC000303065825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303065825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065825 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 27, 27, 4, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 3, 3, 3, 27, 27, 6, 27, 3, 3, 3, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/7 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/7' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1) `ZINC000303065825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303065825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065825 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 8, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 3, 3, 3, 24, 24, 9, 24, 3, 3, 3, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303065825 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 Building ZINC000303065825 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303065825 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 6) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1) `ZINC000303065825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303065825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065825 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 27, 27, 4, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 2, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 8, 8, 6, 8, 8, 6, 3, 3, 3, 27, 27, 6, 27, 3, 3, 3, 6, 6, 6, 6, 6, 8, 8, 8, 8, 8, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 7) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1) `ZINC000303065825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303065825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065825 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 8, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 2, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 7, 10, 10, 7, 3, 3, 3, 24, 24, 9, 24, 3, 3, 3, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 7, 7] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303065825 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065825 Building ZINC000303065826 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303065826 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/8 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1) `ZINC000303065826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303065826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065826 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 21, 21, 2, 21, 21, 21, 21, 21, 21, 2, 2, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 2, 2, 2, 21, 21, 3, 21, 2, 2, 2, 8, 8, 8, 8, 8, 9, 9, 8, 9, 9, 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]) total number of confs: 71 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/9 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/9' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1) `ZINC000303065826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303065826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065826 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 8, 8, 8, 8, 8, 10, 10, 8, 10, 10, 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]) total number of confs: 65 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303065826 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 Building ZINC000303065826 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303065826 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 8) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1) `ZINC000303065826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303065826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065826 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 21, 21, 2, 21, 21, 21, 21, 21, 21, 2, 2, 1, 1, 1, 2, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 8, 9, 9, 8, 2, 2, 2, 21, 21, 3, 21, 2, 2, 2, 8, 8, 8, 8, 8, 9, 9, 8, 9, 9, 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]) total number of confs: 71 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 9) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1) `ZINC000303065826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303065826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065826 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@@H](C)O[C@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 8, 8, 8, 8, 10, 10, 8, 10, 10, 8, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 8, 8, 8, 8, 8, 10, 10, 8, 10, 10, 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]) total number of confs: 65 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303065826 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065826 Building ZINC000303065827 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303065827 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/10 `/scratch/xiaobo/281161/xco-8058088.67/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)N1C[C@H](C)O[C@@H](c2ccccc2)C1) `ZINC000303065827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303065827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065827 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 5, 7, 7, 5, 3, 3, 3, 26, 26, 3, 26, 3, 3, 3, 5, 5, 5, 5, 5, 7, 7, 5, 7, 7, 5, 5] 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: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/11 `/scratch/xiaobo/281161/xco-8058088.67/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)N1C[C@H](C)O[C@@H](c2ccccc2)C1) `ZINC000303065827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303065827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065827 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 8, 11, 11, 8, 3, 3, 3, 20, 20, 9, 20, 3, 3, 3, 8, 8, 8, 8, 8, 11, 11, 8, 11, 11, 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]) total number of confs: 89 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303065827 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 Building ZINC000303065827 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303065827 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 10) grep: /scratch/xiaobo/281161/xco-8058088.67/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)N1C[C@H](C)O[C@@H](c2ccccc2)C1) `ZINC000303065827.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303065827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065827 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 5, 7, 7, 5, 3, 3, 3, 26, 26, 3, 26, 3, 3, 3, 5, 5, 5, 5, 5, 7, 7, 5, 7, 7, 5, 5] 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: 79 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 11) grep: /scratch/xiaobo/281161/xco-8058088.67/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)N1C[C@H](C)O[C@@H](c2ccccc2)C1) `ZINC000303065827.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303065827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303065827 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1C[C@H](C)O[C@@H](c2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 2, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 11, 11, 8, 11, 11, 8, 3, 3, 3, 20, 20, 9, 20, 3, 3, 3, 8, 8, 8, 8, 8, 11, 11, 8, 11, 11, 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]) total number of confs: 89 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303065827 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303065827 Building ZINC000303088291 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303088291 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/12 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1C(=O)N1CCCCC1) `ZINC000303088291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303088291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000303088291 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1C(=O)N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 9, 9, 9, 8, 9, 9, 12, 24, 30, 30, 30, 30, 30, 30, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 5, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/13 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/13' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1C(=O)N1CCCCC1) `ZINC000303088291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303088291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000303088291 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1C(=O)N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 5, 9, 9, 11, 25, 31, 31, 31, 31, 31, 31, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303088291 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 Building ZINC000303088291 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303088291 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 12) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1C(=O)N1CCCCC1) `ZINC000303088291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303088291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000303088291 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1C(=O)N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 9, 9, 9, 8, 9, 9, 12, 24, 30, 30, 30, 30, 30, 30, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 5, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 13) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1C(=O)N1CCCCC1) `ZINC000303088291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303088291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000303088291 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1C(=O)N1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 7, 7, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 5, 9, 9, 11, 25, 31, 31, 31, 31, 31, 31, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303088291 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303088291 Building ZINC000303319633 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303319633 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/14 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(COc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cc2)no1) `ZINC000303319633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303319633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000303319633 none Cc1nc(COc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', '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, 1, 8, 1, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 8, 12, 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, 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, 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: [10, 10, 10, 2, 2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 10, 10, 10, 2, 2, 2, 2, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/15 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/15' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(COc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cc2)no1) `ZINC000303319633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303319633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000303319633 none Cc1nc(COc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', '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, 1, 8, 1, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 8, 12, 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, 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, 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: [10, 10, 10, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 10, 10, 10, 2, 2, 2, 2, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303319633 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 Building ZINC000303319633 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303319633 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 14) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nc(COc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cc2)no1) `ZINC000303319633.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303319633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000303319633 none Cc1nc(COc2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', '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, 1, 8, 1, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 8, 12, 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, 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, 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: [10, 10, 10, 2, 2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 10, 10, 10, 2, 2, 2, 2, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 15) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nc(COc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cc2)no1) `ZINC000303319633.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303319633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000303319633 none Cc1nc(COc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.2', '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, 1, 8, 1, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 8, 12, 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, 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, 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: [10, 10, 10, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 10, 10, 10, 10, 10, 2, 2, 2, 2, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303319633 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303319633 Building ZINC000915078021 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000915078021 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/16 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1NC(=O)OC(C)(C)C) `ZINC000915078021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000915078021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000915078021 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 21, 23, 23, 25, 25, 25, 25, 13, 13, 13, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25] 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/17 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/17' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1NC(=O)OC(C)(C)C) `ZINC000915078021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000915078021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000915078021 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 22, 24, 24, 26, 26, 26, 26, 12, 12, 12, 5, 5, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 5, 22, 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, 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/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000915078021 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 Building ZINC000915078021 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000915078021 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 16) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1NC(=O)OC(C)(C)C) `ZINC000915078021.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000915078021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000915078021 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 21, 23, 23, 25, 25, 25, 25, 13, 13, 13, 5, 5, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 5, 21, 25, 25, 25, 25, 25, 25, 25, 25, 25] 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: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 17) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1NC(=O)OC(C)(C)C) `ZINC000915078021.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000915078021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000915078021 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 5, 5, 5, 22, 24, 24, 26, 26, 26, 26, 12, 12, 12, 5, 5, 2, 2, 2, 2, 4, 4, 3, 4, 4, 2, 2, 2, 5, 22, 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, 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/281161/xco-8058088.67/working/building/ZINC000915078021 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000915078021 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915078021 Building ZINC000915151266 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000915151266 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/18 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)ccc1F) `ZINC000915151266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000915151266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000915151266 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 22, 31, 31, 36, 36, 36, 36, 5, 5, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 5, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/19 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/19' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)ccc1F) `ZINC000915151266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000915151266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000915151266 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 21, 29, 29, 37, 37, 37, 37, 5, 5, 5, 5, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 5, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000915151266 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 Building ZINC000915151266 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000915151266 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 18) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)ccc1F) `ZINC000915151266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000915151266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000915151266 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 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, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 22, 31, 31, 36, 36, 36, 36, 5, 5, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 5, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 19) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)ccc1F) `ZINC000915151266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000915151266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000915151266 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(NC(=O)OC(C)(C)C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 21, 29, 29, 37, 37, 37, 37, 5, 5, 5, 5, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 5, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 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/281161/xco-8058088.67/working/building/ZINC000915151266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000915151266 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915151266 Building ZINC000009803132 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000009803132 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/20 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1F) `ZINC000009803132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000009803132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000009803132 none COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 22, 22, 22, 30, 30, 30, 22, 22, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/21 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/21' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1F) `ZINC000009803132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000009803132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000009803132 none COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 22, 22, 22, 30, 30, 30, 22, 22, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 22] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000009803132 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 Building ZINC000009803132 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000009803132 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 20) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1F) `ZINC000009803132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000009803132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000009803132 none COc1ccc(c2csc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 22, 22, 22, 30, 30, 30, 22, 22, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 22] 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]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 21) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1F) `ZINC000009803132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000009803132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000009803132 none COc1ccc(c2csc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)n2)cc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 15, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 22, 22, 22, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 22, 22, 22, 30, 30, 30, 22, 22, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 22] 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000009803132 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009803132 Building ZINC000915866538 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000915866538 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/22 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1) `ZINC000915866538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000915866538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000915866538 none Cc1nc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [11, 11, 11, 5, 5, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 5, 5, 5, 5, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/23 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/23' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1) `ZINC000915866538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000915866538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000915866538 none Cc1nc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [11, 11, 11, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 5, 5, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000915866538 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 Building ZINC000915866538 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000915866538 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 22) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1) `ZINC000915866538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000915866538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000915866538 none Cc1nc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [11, 11, 11, 5, 5, 5, 4, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 5, 5, 5, 5, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 23) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1) `ZINC000915866538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000915866538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000915866538 none Cc1nc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [11, 11, 11, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 11, 11, 11, 11, 11, 5, 5, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000915866538 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915866538 Building ZINC000915874156 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000915874156 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/24 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/24' -> `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(C)nn(c3ccccc3)c2C)c1) `ZINC000915874156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000915874156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000915874156 none COc1ccc(NC(=O)OC(C)(C)C)c(NC(=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', '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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 12, 20, 20, 32, 32, 32, 32, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 9, 9, 9, 6, 6, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/25 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/25' -> `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(C)nn(c3ccccc3)c2C)c1) `ZINC000915874156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000915874156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000915874156 none COc1ccc(NC(=O)OC(C)(C)C)c(NC(=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', '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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 14, 22, 22, 31, 31, 31, 31, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 6, 9, 9, 9, 6, 6, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000915874156 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 Building ZINC000915874156 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000915874156 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 24) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000915874156.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000915874156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000915874156 none COc1ccc(NC(=O)OC(C)(C)C)c(NC(=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', '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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 12, 20, 20, 32, 32, 32, 32, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 9, 9, 9, 6, 6, 12, 32, 32, 32, 32, 32, 32, 32, 32, 32, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 25) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(NC(=O)OC(C)(C)C)c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000915874156.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000915874156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000915874156 none COc1ccc(NC(=O)OC(C)(C)C)c(NC(=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', '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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 14, 22, 22, 31, 31, 31, 31, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 6, 9, 9, 9, 6, 6, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000915874156 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000915874156 Building ZINC000010882266 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000010882266 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/26 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/26' -> `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)NCc1coc(c2cccs2)n1) `ZINC000010882266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000010882266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000010882266 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1coc(c2cccs2)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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 14, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 16, 16, 16, 16, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 12, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/27 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/27' -> `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)NCc1coc(c2cccs2)n1) `ZINC000010882266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000010882266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000010882266 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1coc(c2cccs2)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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 14, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 18, 18, 18, 18, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 14, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000010882266 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 Building ZINC000010882266 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000010882266 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 26) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1coc(c2cccs2)n1) `ZINC000010882266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000010882266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000010882266 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1coc(c2cccs2)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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 14, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 12, 12, 16, 16, 16, 16, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 12, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 27) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1coc(c2cccs2)n1) `ZINC000010882266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000010882266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000010882266 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1coc(c2cccs2)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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 14, 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, 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] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 18, 18, 18, 18, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 14, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000010882266 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010882266 Building ZINC000916062280 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916062280 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/28 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/28' -> `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(N2C(=O)c3ccccc3C2=O)c(Cl)c1) `ZINC000916062280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916062280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000916062280 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 4, 17, 17, 14, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 17, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 4, 17, 17, 34, 34, 34, 34, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/29 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/29' -> `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(N2C(=O)c3ccccc3C2=O)c(Cl)c1) `ZINC000916062280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916062280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000916062280 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 14, 14, 28, 28, 28, 28, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916062280 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 Building ZINC000916062280 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916062280 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 28) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1) `ZINC000916062280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916062280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000916062280 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 4, 17, 17, 14, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17, 17, 17, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 4, 17, 17, 34, 34, 34, 34, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 29) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1) `ZINC000916062280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916062280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000916062280 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2C(=O)c3ccccc3C2=O)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 1, 16, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 14, 14, 28, 28, 28, 28, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916062280 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916062280 Building ZINC000916068498 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916068498 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/30 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000916068498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916068498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000916068498 none CCOC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 5, 9, 3, 2, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 10, 10, 10, 10, 10, 5, 3, 3, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/31 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/31' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000916068498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916068498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000916068498 none CCOC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 11, 8, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 12, 12, 12, 12, 12, 8, 2, 2, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916068498 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 Building ZINC000916068498 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916068498 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 30) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000916068498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916068498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000916068498 none CCOC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 5, 9, 3, 2, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 10, 10, 10, 10, 10, 5, 3, 3, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 3, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 31) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000916068498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916068498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000916068498 none CCOC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 11, 8, 11, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 2, 2, 12, 12, 12, 12, 12, 8, 2, 2, 1, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916068498 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916068498 Building ZINC000916431120 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916431120 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/32 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1NC(=O)OC(C)(C)C) `ZINC000916431120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916431120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000916431120 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 18, 25, 25, 31, 32, 32, 32, 10, 10, 10, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/33 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/33' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1NC(=O)OC(C)(C)C) `ZINC000916431120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916431120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000916431120 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 18, 24, 24, 31, 32, 32, 32, 10, 10, 10, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916431120 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 Building ZINC000916431120 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916431120 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 32) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1NC(=O)OC(C)(C)C) `ZINC000916431120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916431120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000916431120 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 18, 25, 25, 31, 32, 32, 32, 10, 10, 10, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 33) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1NC(=O)OC(C)(C)C) `ZINC000916431120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916431120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000916431120 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1NC(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 18, 24, 24, 31, 32, 32, 32, 10, 10, 10, 6, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 18, 32, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916431120 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916431120 Building ZINC000916463714 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916463714 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/34 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/34' -> `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(=O)n(Cc2ccccc2)c1) `ZINC000916463714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916463714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000916463714 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(=O)n(Cc2ccccc2)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 9, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/35 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/35' -> `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(=O)n(Cc2ccccc2)c1) `ZINC000916463714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916463714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000916463714 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(=O)n(Cc2ccccc2)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 7, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 2, 7, 7, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916463714 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 Building ZINC000916463714 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916463714 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 34) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(=O)n(Cc2ccccc2)c1) `ZINC000916463714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916463714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000916463714 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(=O)n(Cc2ccccc2)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 9, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 9, 9, 12, 12, 12, 12, 12, 12, 12, 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]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 35) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(=O)n(Cc2ccccc2)c1) `ZINC000916463714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916463714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000916463714 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(=O)n(Cc2ccccc2)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.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 7, 2, 2, 2, 8, 8, 3, 8, 2, 2, 2, 2, 7, 7, 12, 12, 12, 12, 12, 12, 12, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916463714 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916463714 Building ZINC000916474861 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916474861 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/36 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000916474861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916474861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000916474861 none COC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need 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, 4, 8, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 4, 2, 2, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/37 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/37' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000916474861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916474861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000916474861 none COC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need 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, 4, 8, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 4, 2, 2, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916474861 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 Building ZINC000916474861 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916474861 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 36) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000916474861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916474861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000916474861 none COC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need 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, 4, 8, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 4, 2, 2, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 37) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000916474861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916474861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000916474861 none COC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need 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, 4, 8, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 4, 2, 2, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 2] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916474861 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916474861 Building ZINC000916499046 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916499046 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/38 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)c1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000916499046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916499046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000916499046 none CCNC(=O)c1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 8, 4, 4, 2, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 8, 4, 4, 4, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 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: 69 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/39 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/39' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)c1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000916499046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916499046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000916499046 none CCNC(=O)c1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 8, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 8, 4, 4, 4, 2, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2] 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: 66 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916499046 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 Building ZINC000916499046 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000916499046 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 38) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCNC(=O)c1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000916499046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000916499046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000916499046 none CCNC(=O)c1ccc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 8, 4, 4, 2, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 8, 4, 4, 4, 2, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2] 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: 69 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 39) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCNC(=O)c1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000916499046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000916499046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC000916499046 none CCNC(=O)c1ccc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 4, 8, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 10, 10, 10, 10, 10, 8, 4, 4, 4, 2, 2, 2, 2, 12, 12, 4, 12, 2, 2, 2] 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: 66 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000916499046 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000916499046 Building ZINC000497328750 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497328750 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/40 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCCCC2=O)c1) `ZINC000497328750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497328750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000497328750 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCCCC2=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/41 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/41' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCCCC2=O)c1) `ZINC000497328750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497328750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000497328750 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCCCC2=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 5, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000497328750 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 Building ZINC000497328750 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497328750 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 40) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCCCC2=O)c1) `ZINC000497328750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497328750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000497328750 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCCCC2=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 41) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/41: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCCCC2=O)c1) `ZINC000497328750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497328750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000497328750 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN2CCCCC2=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 5, 5, 5, 5, 1, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 5, 3, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC000497328750 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000497328750 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497328750 Building ZINC000497355401 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497355401 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/42 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/42' -> `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)NCc1cccc(OC(F)F)c1) `ZINC000497355401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497355401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000497355401 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 18, 18, 18, 10, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2, 2, 4, 4, 11, 11, 11, 18, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/43 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/43' -> `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)NCc1cccc(OC(F)F)c1) `ZINC000497355401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497355401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000497355401 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 12, 12, 12, 12, 12, 20, 20, 20, 11, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 2, 5, 5, 12, 12, 12, 20, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000497355401 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 Building ZINC000497355401 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497355401 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 42) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(OC(F)F)c1) `ZINC000497355401.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497355401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000497355401 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 18, 18, 18, 10, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2, 2, 4, 4, 11, 11, 11, 18, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 43) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(OC(F)F)c1) `ZINC000497355401.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497355401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000497355401 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 12, 12, 12, 12, 12, 20, 20, 20, 11, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 2, 5, 5, 12, 12, 12, 20, 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000497355401 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497355401 Building ZINC000917112983 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917112983 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/44 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN(C)C(=O)OC(C)(C)C)c1) `ZINC000917112983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917112983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000917112983 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN(C)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 17, 29, 29, 48, 48, 50, 50, 50, 50, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 7, 17, 17, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/45 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/45' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN(C)C(=O)OC(C)(C)C)c1) `ZINC000917112983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917112983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000917112983 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN(C)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 17, 29, 29, 48, 48, 50, 50, 50, 50, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 7, 17, 17, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917112983 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 Building ZINC000917112983 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917112983 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 44) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/44: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN(C)C(=O)OC(C)(C)C)c1) `ZINC000917112983.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917112983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000917112983 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CN(C)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 7, 7, 17, 29, 29, 48, 48, 50, 50, 50, 50, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 7, 17, 17, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 45) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/45: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN(C)C(=O)OC(C)(C)C)c1) `ZINC000917112983.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917112983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000917112983 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CN(C)C(=O)OC(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 8, 5, 1, 11, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 17, 29, 29, 48, 48, 50, 50, 50, 50, 7, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 7, 7, 7, 17, 17, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917112983 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917112983 Building ZINC000497584012 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497584012 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/46 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/46' -> `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)NCCc1c[nH]c2cc(F)ccc12) `ZINC000497584012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497584012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000497584012 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.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: [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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 9, 9, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/47 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/47' -> `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)NCCc1c[nH]c2cc(F)ccc12) `ZINC000497584012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497584012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000497584012 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.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: [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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 10, 10, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000497584012 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 Building ZINC000497584012 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497584012 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 46) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)ccc12) `ZINC000497584012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497584012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000497584012 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.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: [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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 9, 9, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 47) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)ccc12) `ZINC000497584012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497584012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000497584012 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1c[nH]c2cc(F)ccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.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: [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, 8, 6, 1, 1, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 10, 10, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000497584012 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497584012 Building ZINC000917490091 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917490091 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/48 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/48' -> `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)Cc1ccn(c2ccccc2)n1) `ZINC000917490091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917490091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000917490091 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccn(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 5, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/49 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/49' -> `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)Cc1ccn(c2ccccc2)n1) `ZINC000917490091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917490091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000917490091 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccn(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917490091 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 Building ZINC000917490091 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917490091 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 48) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccn(c2ccccc2)n1) `ZINC000917490091.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917490091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000917490091 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)Cc1ccn(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 5, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 49) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccn(c2ccccc2)n1) `ZINC000917490091.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917490091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000917490091 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)Cc1ccn(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917490091 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917490091 Building ZINC000917705967 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917705967 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/50 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/50' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000917705967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917705967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000917705967 none COC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 11, 8, 2, 2, 2, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2] 50 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/51 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/51' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000917705967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917705967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000917705967 none COC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 11, 8, 2, 2, 2, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2] 50 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917705967 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 Building ZINC000917705967 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917705967 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 50) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000917705967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917705967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000917705967 none COC(=O)Nc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 11, 8, 2, 2, 2, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2] 50 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 51) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000917705967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917705967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000917705967 none COC(=O)Nc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 11, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 11, 11, 11, 8, 2, 2, 2, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2] 50 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917705967 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917705967 Building ZINC000917796891 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917796891 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/52 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/52' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(N2CCCC2=O)ccc1F) `ZINC000917796891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917796891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000917796891 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(N2CCCC2=O)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 8, 8, 9, 9, 9, 9, 9, 8, 8, 8, 8, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 8, 9, 9, 9, 9, 9, 9, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/53 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/53' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(N2CCCC2=O)ccc1F) `ZINC000917796891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917796891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000917796891 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(N2CCCC2=O)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 7, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917796891 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 Building ZINC000917796891 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917796891 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 52) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/52: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(N2CCCC2=O)ccc1F) `ZINC000917796891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917796891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000917796891 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(N2CCCC2=O)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 8, 8, 8, 9, 9, 9, 9, 9, 8, 8, 8, 8, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 8, 9, 9, 9, 9, 9, 9, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 53) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/53: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(N2CCCC2=O)ccc1F) `ZINC000917796891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917796891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000917796891 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(N2CCCC2=O)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 7, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 53 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917796891 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917796891 Building ZINC000009989437 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000009989437 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/54 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/54' -> `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(=O)c2ccccc2)CC1) `ZINC000009989437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000009989437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000009989437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccccc2)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', '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'] dock atom type 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, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 11, 11, 12, 12, 12, 12, 12, 4, 4, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/55 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/55' -> `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(=O)c2ccccc2)CC1) `ZINC000009989437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000009989437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000009989437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccccc2)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', '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'] dock atom type 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, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000009989437 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 Building ZINC000009989437 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000009989437 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 54) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccccc2)CC1) `ZINC000009989437.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000009989437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000009989437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccccc2)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', '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'] dock atom type 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, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 11, 11, 12, 12, 12, 12, 12, 4, 4, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 49 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 55) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccccc2)CC1) `ZINC000009989437.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000009989437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000009989437 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccccc2)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', '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'] dock atom type 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, 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] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 9, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000009989437 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000009989437 Building ZINC000917805824 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917805824 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/56 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/56' -> `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)Nc1ccccc1C(=O)N(C)C1CCCCC1) `ZINC000917805824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917805824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000917805824 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 14, 14, 29, 29, 33, 33, 33, 33, 33, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 2, 6, 6, 6, 6, 29, 29, 29, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/57 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/57' -> `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)Nc1ccccc1C(=O)N(C)C1CCCCC1) `ZINC000917805824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917805824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000917805824 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 14, 14, 30, 30, 34, 34, 34, 34, 34, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 6, 6, 6, 6, 30, 30, 30, 34, 34, 34, 34, 34, 34, 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]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917805824 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 Building ZINC000917805824 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000917805824 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 56) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/56: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N(C)C1CCCCC1) `ZINC000917805824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000917805824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000917805824 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 14, 14, 29, 29, 33, 33, 33, 33, 33, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 2, 6, 6, 6, 6, 29, 29, 29, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 122 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 57) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/57: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N(C)C1CCCCC1) `ZINC000917805824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000917805824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000917805824 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 14, 14, 30, 30, 34, 34, 34, 34, 34, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 2, 6, 6, 6, 6, 30, 30, 30, 34, 34, 34, 34, 34, 34, 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]) total number of confs: 120 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000917805824 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000917805824 Building ZINC000497899773 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497899773 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/58 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/58' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3ncccc23)CC1) `ZINC000497899773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497899773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000497899773 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3ncccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 6, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 3, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4, 4, 13, 13, 13, 13, 4, 4, 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/59 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/59' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3ncccc23)CC1) `ZINC000497899773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497899773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000497899773 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3ncccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 6, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 3, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 13, 13, 13, 13, 4, 4, 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]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000497899773 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 Building ZINC000497899773 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000497899773 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 58) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3ncccc23)CC1) `ZINC000497899773.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000497899773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000497899773 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3ncccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 6, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 3, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4, 4, 4, 13, 13, 13, 13, 4, 4, 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]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 59) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3ncccc23)CC1) `ZINC000497899773.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000497899773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000497899773 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2c[nH]c3ncccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 6, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 3, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 13, 13, 13, 13, 4, 4, 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]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000497899773 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000497899773 Building ZINC000498202871 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498202871 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/60 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)C1CC1) `ZINC000498202871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498202871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000498202871 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 17, 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] dock 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, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 22, 22, 21, 22, 22, 22, 5, 8, 8, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 9, 9, 22, 22, 22, 22, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/61 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/61' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)C1CC1) `ZINC000498202871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498202871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000498202871 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 17, 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] dock 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, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 5, 9, 25, 25, 25, 25, 25, 24, 5, 8, 8, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 9, 9, 25, 25, 25, 25, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 91 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000498202871 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 Building ZINC000498202871 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498202871 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 60) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/60: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)C1CC1) `ZINC000498202871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498202871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000498202871 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 17, 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] dock 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, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 5, 9, 22, 22, 21, 22, 22, 22, 5, 8, 8, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 9, 9, 22, 22, 22, 22, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 89 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 61) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/61: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)C1CC1) `ZINC000498202871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498202871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000498202871 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cccc(Br)c1)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 17, 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] dock 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, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 5, 9, 25, 25, 25, 25, 25, 24, 5, 8, 8, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 9, 9, 25, 25, 25, 25, 8, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 91 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000498202871 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498202871 Building ZINC000918615215 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000918615215 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/62 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000918615215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000918615215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000918615215 none CC(C)(C)OC(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 23, 9, 9, 9, 7, 9, 9, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 9, 9, 9, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/63 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/63' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000918615215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000918615215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000918615215 none CC(C)(C)OC(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 21, 9, 9, 9, 7, 9, 9, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 9, 9, 9, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000918615215 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 Building ZINC000918615215 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000918615215 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 62) grep: /scratch/xiaobo/281161/xco-8058088.67/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)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000918615215.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000918615215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000918615215 none CC(C)(C)OC(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 23, 9, 9, 9, 7, 9, 9, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 9, 9, 9, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 63) grep: /scratch/xiaobo/281161/xco-8058088.67/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)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1) `ZINC000918615215.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000918615215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC000918615215 none CC(C)(C)OC(=O)Nc1ccc(C(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1cnn(C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 21, 9, 9, 9, 7, 9, 9, 9, 9, 9, 9, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16, 9, 9, 9, 2, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000918615215 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000918615215 Building ZINC000498452117 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498452117 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/64 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2ccccc2)c1C) `ZINC000498452117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498452117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000498452117 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 25, 25, 25, 36, 36, 29, 36, 36, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 7, 7, 7, 25, 36, 36, 36, 36, 36, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/65 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/65' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2ccccc2)c1C) `ZINC000498452117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498452117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000498452117 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 24, 24, 24, 34, 34, 24, 34, 34, 7, 7, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 7, 7, 7, 24, 34, 34, 24, 34, 34, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000498452117 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 Building ZINC000498452117 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498452117 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 64) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2ccccc2)c1C) `ZINC000498452117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498452117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000498452117 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 25, 25, 25, 36, 36, 29, 36, 36, 7, 7, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 7, 7, 7, 25, 36, 36, 36, 36, 36, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 65) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2ccccc2)c1C) `ZINC000498452117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498452117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000498452117 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 24, 24, 24, 34, 34, 24, 34, 34, 7, 7, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 7, 7, 7, 24, 34, 34, 24, 34, 34, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000498452117 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498452117 Building ZINC000498478060 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498478060 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/66 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/66' -> `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(C(=O)N2CCc3ccccc32)cc1) `ZINC000498478060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498478060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000498478060 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 31, 32, 39, 40, 40, 41, 41, 41, 41, 40, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 39, 39, 40, 40, 41, 41, 41, 40, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/67 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/67' -> `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(C(=O)N2CCc3ccccc32)cc1) `ZINC000498478060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498478060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000498478060 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 4, 7, 31, 32, 40, 40, 41, 41, 41, 41, 41, 41, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 40, 40, 40, 40, 41, 41, 41, 41, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000498478060 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 Building ZINC000498478060 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000498478060 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 66) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCc3ccccc32)cc1) `ZINC000498478060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000498478060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000498478060 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 31, 32, 39, 40, 40, 41, 41, 41, 41, 40, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 39, 39, 40, 40, 41, 41, 41, 40, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 67) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCc3ccccc32)cc1) `ZINC000498478060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000498478060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000498478060 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCc3ccccc32)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 4, 7, 31, 32, 40, 40, 41, 41, 41, 41, 41, 41, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 40, 40, 40, 40, 41, 41, 41, 41, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000498478060 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000498478060 Building ZINC000072035106 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000072035106 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/68 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/68' -> `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(CCCN(C)C)Cc1ccc(Cl)c(Cl)c1) `ZINC000072035106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000072035106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000072035106 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)Cc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 10, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 4, 9, 9, 15, 21, 21, 4, 9, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 9, 9, 9, 9, 15, 15, 21, 21, 21, 21, 21, 21, 9, 9, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 148 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/69 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/69' -> `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(CCCN(C)C)Cc1ccc(Cl)c(Cl)c1) `ZINC000072035106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000072035106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000072035106 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)Cc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 10, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 4, 8, 8, 14, 17, 17, 4, 7, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 8, 8, 8, 8, 14, 14, 17, 17, 17, 17, 17, 17, 7, 7, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 113 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000072035106 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 Building ZINC000072035106 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000072035106 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 68) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)Cc1ccc(Cl)c(Cl)c1) `ZINC000072035106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000072035106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000072035106 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CCCN(C)C)Cc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 10, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 4, 9, 9, 15, 21, 21, 4, 9, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 6, 6, 3, 6, 6, 2, 2, 2, 9, 9, 9, 9, 15, 15, 21, 21, 21, 21, 21, 21, 9, 9, 19, 19, 19] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 148 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 69) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)Cc1ccc(Cl)c(Cl)c1) `ZINC000072035106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000072035106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000072035106 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CCCN(C)C)Cc1ccc(Cl)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 10, 5, 5, 5, 1, 1, 1, 1, 16, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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] 0 hydrogens need rotated 50 conformations in 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, 4, 8, 8, 14, 17, 17, 4, 7, 15, 15, 15, 15, 15, 15, 15, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 8, 8, 8, 8, 14, 14, 17, 17, 17, 17, 17, 17, 7, 7, 15, 15, 15] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 113 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000072035106 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000072035106 Building ZINC000649212583 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649212583 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/70 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2cccc(C(F)(F)F)c2)n1) `ZINC000649212583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649212583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000649212583 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2cccc(C(F)(F)F)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 13, 13, 33, 33, 13, 33, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 33, 33, 27, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 122 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/71 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/71' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2cccc(C(F)(F)F)c2)n1) `ZINC000649212583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649212583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000649212583 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2cccc(C(F)(F)F)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 14, 14, 34, 34, 14, 34, 34, 34, 34, 34, 34, 14, 14, 14, 14, 14, 5, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 34, 34, 14, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000649212583 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 Building ZINC000649212583 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649212583 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 70) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2cccc(C(F)(F)F)c2)n1) `ZINC000649212583.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649212583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000649212583 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2cccc(C(F)(F)F)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 13, 13, 33, 33, 13, 33, 33, 33, 33, 33, 33, 13, 13, 13, 13, 13, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 33, 33, 27, 33] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 122 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 71) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2cccc(C(F)(F)F)c2)n1) `ZINC000649212583.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649212583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000649212583 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2cccc(C(F)(F)F)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 14, 14, 34, 34, 14, 34, 34, 34, 34, 34, 34, 14, 14, 14, 14, 14, 5, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 34, 34, 14, 34] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 107 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000649212583 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649212583 Building ZINC000919681782 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000919681782 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/72 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)c2c3c(sc2NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC3)cc1) `ZINC000919681782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000919681782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000919681782 none COc1ccc(NC(=O)c2c3c(sc2NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC3)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.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 7, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 8, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/73 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/73' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(NC(=O)c2c3c(sc2NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC3)cc1) `ZINC000919681782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000919681782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000919681782 none COc1ccc(NC(=O)c2c3c(sc2NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC3)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.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 10, 10, 10, 7, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000919681782 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 Building ZINC000919681782 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000919681782 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 72) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(NC(=O)c2c3c(sc2NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC3)cc1) `ZINC000919681782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000919681782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000919681782 none COc1ccc(NC(=O)c2c3c(sc2NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC3)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.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 11, 11, 11, 7, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 8, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 73) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(NC(=O)c2c3c(sc2NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC3)cc1) `ZINC000919681782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000919681782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000919681782 none COc1ccc(NC(=O)c2c3c(sc2NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)CCCC3)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.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 10, 10, 10, 7, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 8, 4, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000919681782 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919681782 Building ZINC000919770431 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000919770431 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/74 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000919770431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000919770431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000919770431 none CCOC(=O)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 8, 11, 1, 8, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 15, 15, 15, 15, 15, 8, 8, 8, 3, 3, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 3, 3] 50 rigid atoms, others: [10, 11, 12, 45, 14, 13, 16, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/75 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/75' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000919770431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000919770431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000919770431 none CCOC(=O)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 11, 11, 10, 11, 3, 10, 3, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 13, 13, 13, 13, 13, 10, 10, 10, 4, 4, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000919770431 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431 Building ZINC000919770431 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000919770431 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 74) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOC(=O)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000919770431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000919770431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000919770431 none CCOC(=O)N(C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 11, 8, 11, 1, 8, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 15, 15, 15, 15, 15, 8, 8, 8, 3, 3, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 3, 3] 50 rigid atoms, others: [10, 11, 12, 45, 14, 13, 16, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 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/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 75) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOC(=O)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000919770431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000919770431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000919770431 none CCOC(=O)N(C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 0 hydrogens 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, 11, 11, 10, 11, 3, 10, 3, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 13, 13, 13, 13, 13, 10, 10, 10, 4, 4, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/281161/xco-8058088.67/working/building/ZINC000919770431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000919770431 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000919770431 Building ZINC000499053086 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499053086 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/76 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/76' -> `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(Cc1cc(Br)ccc1F)C1CC1) `ZINC000499053086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499053086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499053086 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cc(Br)ccc1F)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 8, 3, 3, 1, 1, 1, 1, 4, 4, 7, 15, 23, 23, 23, 21, 23, 23, 23, 7, 9, 9, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 23, 23, 23, 9, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/77 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/77' -> `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(Cc1cc(Br)ccc1F)C1CC1) `ZINC000499053086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499053086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499053086 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cc(Br)ccc1F)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 8, 17, 28, 28, 28, 23, 28, 28, 28, 8, 12, 12, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 3, 17, 17, 28, 23, 28, 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]) total number of confs: 131 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499053086 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 Building ZINC000499053086 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499053086 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 76) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cc(Br)ccc1F)C1CC1) `ZINC000499053086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499053086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499053086 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1cc(Br)ccc1F)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 8, 8, 3, 3, 1, 1, 1, 1, 4, 4, 7, 15, 23, 23, 23, 21, 23, 23, 23, 7, 9, 9, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 15, 15, 23, 23, 23, 9, 9, 9, 9, 9] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 102 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 77) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cc(Br)ccc1F)C1CC1) `ZINC000499053086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499053086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499053086 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1cc(Br)ccc1F)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.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 2, 2, 8, 17, 28, 28, 28, 23, 28, 28, 28, 8, 12, 12, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 3, 17, 17, 28, 23, 28, 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]) total number of confs: 131 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499053086 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499053086 Building ZINC000499075562 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499075562 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/78 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C)n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000499075562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499075562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499075562 none Cc1ccc(C)n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 46 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/79 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/79' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(C)n1C1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000499075562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499075562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499075562 none Cc1ccc(C)n1C1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499075562 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 Building ZINC000499075562 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499075562 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 78) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1ccc(C)n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000499075562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499075562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499075562 none Cc1ccc(C)n1C1CCN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 2, 7, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 2, 9, 9, 4, 9, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 46 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 79) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1ccc(C)n1C1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1) `ZINC000499075562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499075562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499075562 none Cc1ccc(C)n1C1CCN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 6, 2, 6, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 8, 8, 8, 8] 50 rigid atoms, others: [13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 45 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499075562 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499075562 Building ZINC000499117879 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499117879 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/80 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Sc1nccn1C) `ZINC000499117879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499117879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499117879 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Sc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 14, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 27, 33, 33, 33, 33, 33, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 6, 13, 13, 13, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/81 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/81' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Sc1nccn1C) `ZINC000499117879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499117879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499117879 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Sc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 14, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 27, 33, 33, 33, 33, 33, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 6, 13, 13, 13, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499117879 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 Building ZINC000499117879 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499117879 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 80) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Sc1nccn1C) `ZINC000499117879.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499117879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499117879 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Sc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 14, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 27, 33, 33, 33, 33, 33, 3, 3, 3, 10, 10, 6, 10, 10, 3, 3, 3, 6, 13, 13, 13, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 110 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 81) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Sc1nccn1C) `ZINC000499117879.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499117879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499117879 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1Sc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 14, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 6, 13, 13, 13, 27, 33, 33, 33, 33, 33, 3, 3, 3, 11, 11, 3, 11, 11, 3, 3, 3, 6, 13, 13, 13, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 105 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499117879 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499117879 Building ZINC000920012923 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920012923 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/82 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000920012923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920012923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000920012923 none CCN(CC)C(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 9, 4, 8, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/83 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/83' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000920012923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920012923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000920012923 none CCN(CC)C(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 4, 8, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000920012923 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 Building ZINC000920012923 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920012923 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 82) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(CC)C(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000920012923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920012923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000920012923 none CCN(CC)C(=O)c1ccccc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 8, 8, 9, 4, 8, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 83) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(CC)C(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000920012923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920012923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000920012923 none CCN(CC)C(=O)c1ccccc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 4, 8, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000920012923 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920012923 Building ZINC000649235039 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649235039 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/84 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/84' -> `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]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1) `ZINC000649235039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649235039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000649235039 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 10, 10, 2, 6, 6, 6, 34, 34, 18, 34, 34, 34, 34, 34, 34, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 10, 10, 10, 34, 34, 34, 34, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/85 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/85' -> `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]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1) `ZINC000649235039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649235039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000649235039 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 9, 12, 12, 12, 12, 12, 4, 6, 6, 6, 40, 40, 16, 40, 40, 40, 40, 40, 40, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000649235039 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 Building ZINC000649235039 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649235039 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 84) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1) `ZINC000649235039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649235039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000649235039 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 10, 10, 2, 6, 6, 6, 34, 34, 18, 34, 34, 34, 34, 34, 34, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 10, 10, 10, 34, 34, 34, 34, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 115 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 85) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1) `ZINC000649235039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649235039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000649235039 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 9, 12, 12, 12, 12, 12, 4, 6, 6, 6, 40, 40, 16, 40, 40, 40, 40, 40, 40, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 6, 6, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000649235039 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235039 Building ZINC000499242276 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499242276 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/86 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000499242276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499242276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000499242276 none CCCN(Cc1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 4, 2, 4, 14, 23, 23, 23, 23, 23, 23, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 12, 12, 12, 12, 12, 10, 10, 14, 14, 23, 23, 23, 23, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/87 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/87' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000499242276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499242276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000499242276 none CCCN(Cc1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens 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, 4, 2, 4, 12, 21, 21, 15, 21, 21, 21, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 11, 11, 11, 11, 11, 9, 9, 12, 12, 21, 21, 15, 21, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499242276 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 Building ZINC000499242276 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499242276 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 86) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCCN(Cc1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000499242276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499242276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000499242276 none CCCN(Cc1ccccc1Br)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 4, 2, 4, 14, 23, 23, 23, 23, 23, 23, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 12, 12, 12, 12, 12, 10, 10, 14, 14, 23, 23, 23, 23, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 87) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCCN(Cc1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000499242276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499242276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000499242276 none CCCN(Cc1ccccc1Br)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 17, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 7, 7] 0 hydrogens 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, 4, 2, 4, 12, 21, 21, 15, 21, 21, 21, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 11, 11, 11, 11, 11, 9, 9, 12, 12, 21, 21, 15, 21, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499242276 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499242276 Building ZINC000920820088 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920820088 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/88 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Nc2cccc(C(F)(F)F)c2)cn1) `ZINC000920820088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920820088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000920820088 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Nc2cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 10, 8, 8, 26, 26, 22, 26, 26, 26, 26, 26, 26, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 4, 9, 9, 9, 9, 10, 26, 26, 23, 26, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/89 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/89' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Nc2cccc(C(F)(F)F)c2)cn1) `ZINC000920820088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920820088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000920820088 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Nc2cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 10, 8, 8, 22, 22, 8, 22, 22, 22, 22, 22, 22, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 9, 9, 9, 9, 10, 22, 22, 8, 22, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 96 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000920820088 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 Building ZINC000920820088 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920820088 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 88) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/88: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Nc2cccc(C(F)(F)F)c2)cn1) `ZINC000920820088.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920820088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000920820088 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Nc2cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 8, 8, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 10, 8, 8, 26, 26, 22, 26, 26, 26, 26, 26, 26, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 4, 9, 9, 9, 9, 10, 26, 26, 23, 26, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 83 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 89) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/89: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Nc2cccc(C(F)(F)F)c2)cn1) `ZINC000920820088.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920820088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000920820088 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Nc2cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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, 1, 1, 1, 1, 1, 1, 1, 11, 8, 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, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 9, 10, 8, 8, 22, 22, 8, 22, 22, 22, 22, 22, 22, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 9, 9, 9, 9, 10, 22, 22, 8, 22, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 96 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000920820088 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920820088 Building ZINC000920948649 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920948649 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/90 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(N2CCCC2=O)cc1) `ZINC000920948649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920948649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000920948649 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 6, 6, 5, 5, 10, 10, 10, 10, 10, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/91 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/91' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(N2CCCC2=O)cc1) `ZINC000920948649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920948649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000920948649 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 6, 6, 5, 6, 11, 11, 11, 11, 11, 6, 6, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 5, 5, 5, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000920948649 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 Building ZINC000920948649 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920948649 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 90) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/90: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(N2CCCC2=O)cc1) `ZINC000920948649.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920948649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000920948649 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 6, 6, 5, 5, 10, 10, 10, 10, 10, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 62 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 91) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/91: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(N2CCCC2=O)cc1) `ZINC000920948649.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920948649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000920948649 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 6, 6, 5, 6, 11, 11, 11, 11, 11, 6, 6, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 3, 5, 5, 5, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/281161/xco-8058088.67/working/building/ZINC000920948649 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000920948649 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948649 Building ZINC000920948650 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920948650 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/92 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(N2CCCC2=O)cc1) `ZINC000920948650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920948650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000920948650 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 6, 6, 5, 5, 9, 9, 9, 9, 9, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/93 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/93' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(N2CCCC2=O)cc1) `ZINC000920948650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920948650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000920948650 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 5, 7, 10, 10, 10, 10, 10, 7, 7, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000920948650 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 Building ZINC000920948650 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000920948650 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 92) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(N2CCCC2=O)cc1) `ZINC000920948650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000920948650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000920948650 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 6, 6, 5, 5, 9, 9, 9, 9, 9, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 93) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(N2CCCC2=O)cc1) `ZINC000920948650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000920948650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000920948650 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(N2CCCC2=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 5, 7, 10, 10, 10, 10, 10, 7, 7, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 7, 7, 10, 10, 10, 10, 10, 10, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000920948650 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000920948650 Building ZINC000615447627 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615447627 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/94 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)cn1) `ZINC000615447627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615447627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000615447627 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)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', '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', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 10, 10, 6, 10, 10, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 4, 10, 10, 6, 10, 10, 21, 21, 21, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/95 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/95' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)cn1) `ZINC000615447627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615447627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000615447627 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)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', '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', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 9, 5, 9, 9, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 3, 9, 9, 5, 9, 9, 19, 19, 19, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 81 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000615447627 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 Building ZINC000615447627 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615447627 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 94) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)cn1) `ZINC000615447627.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615447627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000615447627 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)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', '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', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 10, 10, 6, 10, 10, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 4, 10, 10, 6, 10, 10, 21, 21, 21, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 78 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 95) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)cn1) `ZINC000615447627.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615447627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000615447627 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)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', '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', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 11, 6, 6, 1, 1, 1, 1, 3, 3, 3, 5, 5, 9, 9, 5, 9, 9, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 3, 9, 9, 5, 9, 9, 19, 19, 19, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 81 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000615447627 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447627 Building ZINC000615447630 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615447630 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/96 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)cn1) `ZINC000615447630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615447630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000615447630 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)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', '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', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 10, 10, 7, 10, 10, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 4, 10, 10, 6, 10, 10, 20, 20, 20, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/97 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/97' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)cn1) `ZINC000615447630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615447630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000615447630 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)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', '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', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 10, 10, 8, 10, 10, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 10, 10, 6, 10, 10, 21, 21, 21, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000615447630 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 Building ZINC000615447630 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615447630 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 96) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)cn1) `ZINC000615447630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615447630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000615447630 none CC(C)(C)n1cc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)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', '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', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 9, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 10, 10, 7, 10, 10, 6, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 4, 10, 10, 6, 10, 10, 20, 20, 20, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 77 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 97) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)cn1) `ZINC000615447630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615447630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000615447630 none CC(C)(C)n1cc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)c2ccc3nc(C(F)(F)F)[nH]c3c2)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', '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', 'C.3', 'F', 'F', 'F', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 8, 6, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 10, 6, 6, 1, 1, 1, 1, 4, 4, 4, 6, 6, 10, 10, 8, 10, 10, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 4, 10, 10, 6, 10, 10, 21, 21, 21, 6] 50 rigid atoms, others: [8, 9, 6, 7] set([0, 1, 2, 3, 4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 84 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000615447630 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615447630 Building ZINC000615746597 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615746597 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/98 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/98' -> `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)cc1NC(=O)c1ccco1) `ZINC000615746597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615746597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000615746597 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1NC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 35, 35, 35, 35, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 3, 12, 12, 12, 21, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/99 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/99' -> `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)cc1NC(=O)c1ccco1) `ZINC000615746597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615746597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000615746597 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1NC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 20, 35, 35, 35, 35, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 3, 12, 12, 12, 20, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000615746597 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 Building ZINC000615746597 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615746597 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 98) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1NC(=O)c1ccco1) `ZINC000615746597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615746597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000615746597 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1NC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 12, 12, 12, 12, 12, 12, 12, 21, 21, 21, 35, 35, 35, 35, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 3, 12, 12, 12, 21, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 99) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1NC(=O)c1ccco1) `ZINC000615746597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615746597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000615746597 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(Cl)cc1NC(=O)c1ccco1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 8, 1, 11, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 20, 20, 20, 35, 35, 35, 35, 3, 3, 3, 10, 10, 4, 10, 10, 3, 3, 3, 3, 12, 12, 12, 20, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 99 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000615746597 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615746597 Building ZINC000615974425 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615974425 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/100 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/100' -> `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(NC(=O)c2ccco2)c(Cl)c1) `ZINC000615974425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615974425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000615974425 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 5, 22, 22, 15, 22, 31, 32, 31, 33, 33, 33, 33, 22, 22, 22, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 5, 22, 22, 32, 33, 33, 33, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/101 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/101' -> `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(NC(=O)c2ccco2)c(Cl)c1) `ZINC000615974425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615974425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000615974425 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 16, 10, 16, 29, 29, 29, 32, 32, 32, 32, 16, 16, 16, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 3, 16, 16, 29, 32, 32, 32, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000615974425 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 Building ZINC000615974425 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000615974425 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 100) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(Cl)c1) `ZINC000615974425.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000615974425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000615974425 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 5, 5, 5, 22, 22, 15, 22, 31, 32, 31, 33, 33, 33, 33, 22, 22, 22, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 5, 22, 22, 32, 33, 33, 33, 22] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 101) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(Cl)c1) `ZINC000615974425.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000615974425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000615974425 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)c2ccco2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 3, 3, 3, 16, 16, 10, 16, 29, 29, 29, 32, 32, 32, 32, 16, 16, 16, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 3, 16, 16, 29, 32, 32, 32, 16] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000615974425 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000615974425 Building ZINC000617177728 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617177728 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/102 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/102' -> `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)Nc1cnn(Cc2ccccc2)c1) `ZINC000617177728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617177728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000617177728 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccccc2)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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 6, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 6, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/103 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/103' -> `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)Nc1cnn(Cc2ccccc2)c1) `ZINC000617177728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617177728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000617177728 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccccc2)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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000617177728 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 Building ZINC000617177728 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617177728 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 102) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccccc2)c1) `ZINC000617177728.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617177728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000617177728 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccccc2)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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 6, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 6, 16, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 103) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccccc2)c1) `ZINC000617177728.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617177728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000617177728 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(Cc2ccccc2)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.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 15, 15, 15, 15, 15, 15, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 15, 15, 15, 15, 15, 15, 15, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000617177728 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617177728 Building ZINC000617229116 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617229116 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/104 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)c(F)c1) `ZINC000617229116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617229116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000617229116 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)c(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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 17, 17, 17, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/105 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/105' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)c(F)c1) `ZINC000617229116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617229116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000617229116 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)c(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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 7, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 13, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000617229116 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 Building ZINC000617229116 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617229116 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 104) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/104: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)c(F)c1) `ZINC000617229116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617229116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000617229116 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)c(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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 17, 17, 17, 17, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 17, 17, 17, 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]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 105) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)c(F)c1) `ZINC000617229116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617229116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000617229116 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)c(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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 1, 1, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 7, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 13, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000617229116 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617229116 Building ZINC000617378562 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617378562 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/106 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCCN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000617378562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617378562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000617378562 none COc1ccc(CCCN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 12, 12, 12, 12, 12, 12, 12, 11, 11, 10, 10, 7, 7, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 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, 57, 58, 59]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/107 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/107' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CCCN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000617378562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617378562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000617378562 none COc1ccc(CCCN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 12, 12, 12, 12, 12, 12, 12, 11, 11, 10, 10, 7, 7, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 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, 57, 58, 59]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000617378562 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 Building ZINC000617378562 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000617378562 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 106) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(CCCN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000617378562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000617378562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000617378562 none COc1ccc(CCCN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 12, 12, 12, 12, 12, 12, 12, 11, 11, 10, 10, 7, 7, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 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, 57, 58, 59]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 107) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(CCCN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000617378562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000617378562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000617378562 none COc1ccc(CCCN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 5, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 12, 12, 12, 12, 12, 12, 12, 11, 11, 10, 10, 7, 7, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 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, 57, 58, 59]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000617378562 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000617378562 Building ZINC000139426817 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000139426817 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/108 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000139426817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000139426817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000139426817 none CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.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, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 8, 8, 8, 8, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/109 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/109' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000139426817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000139426817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000139426817 none CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.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, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 8, 8, 8, 8, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [39, 8, 9, 10, 7, 12, 13, 11] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000139426817 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 Building ZINC000139426817 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000139426817 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 108) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/108: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000139426817.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000139426817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000139426817 none CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.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, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 8, 8, 8, 8, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 109) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/109: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C) `ZINC000139426817.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000139426817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000139426817 none CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.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, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 8, 8, 8, 8, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [39, 8, 9, 10, 7, 12, 13, 11] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000139426817 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000139426817 Building ZINC000619113994 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619113994 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/110 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/110' -> `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)N1CCc2[nH]c3c(cccc3Br)c2C1) `ZINC000619113994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619113994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000619113994 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2[nH]c3c(cccc3Br)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 7, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/111 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/111' -> `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)N1CCc2[nH]c3c(cccc3Br)c2C1) `ZINC000619113994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619113994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000619113994 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2[nH]c3c(cccc3Br)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 5, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000619113994 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 Building ZINC000619113994 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619113994 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 110) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2[nH]c3c(cccc3Br)c2C1) `ZINC000619113994.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619113994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000619113994 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCc2[nH]c3c(cccc3Br)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 7, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 111) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2[nH]c3c(cccc3Br)c2C1) `ZINC000619113994.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619113994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000619113994 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCc2[nH]c3c(cccc3Br)c2C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 6, 1, 1, 1, 1, 1, 1, 17, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 5, 14, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000619113994 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619113994 Building ZINC000619974147 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619974147 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/112 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc(O)cc1) `ZINC000619974147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619974147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000619974147 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 11, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 11, 11, 8, 8, 11, 11, 3, 3, 3, 20, 20, 11, 20, 3, 3, 3, 8, 8, 8, 8, 8, 8, 11, 11, 22, 11, 11] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/113 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/113' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc(O)cc1) `ZINC000619974147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619974147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000619974147 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 12, 12, 10, 11, 12, 12, 3, 3, 3, 17, 17, 10, 17, 3, 3, 3, 10, 10, 10, 10, 10, 10, 12, 12, 24, 12, 12] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 102 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000619974147 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 Building ZINC000619974147 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619974147 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 112) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc(O)cc1) `ZINC000619974147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619974147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000619974147 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 11, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 11, 11, 8, 8, 11, 11, 3, 3, 3, 20, 20, 11, 20, 3, 3, 3, 8, 8, 8, 8, 8, 8, 11, 11, 22, 11, 11] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 93 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 113) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc(O)cc1) `ZINC000619974147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619974147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000619974147 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 10, 10, 12, 12, 10, 11, 12, 12, 3, 3, 3, 17, 17, 10, 17, 3, 3, 3, 10, 10, 10, 10, 10, 10, 12, 12, 24, 12, 12] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 102 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000619974147 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974147 Building ZINC000619974148 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619974148 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/114 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc(O)cc1) `ZINC000619974148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619974148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000619974148 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 12, 12, 10, 10, 12, 12, 3, 3, 3, 18, 18, 10, 18, 3, 3, 3, 10, 10, 10, 10, 10, 10, 12, 12, 24, 12, 12] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 103 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/115 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/115' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc(O)cc1) `ZINC000619974148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619974148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000619974148 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 11, 11, 7, 7, 11, 11, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 11, 22, 11, 11] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000619974148 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 Building ZINC000619974148 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000619974148 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 114) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc(O)cc1) `ZINC000619974148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000619974148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000619974148 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 3, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 12, 12, 10, 10, 12, 12, 3, 3, 3, 18, 18, 10, 18, 3, 3, 3, 10, 10, 10, 10, 10, 10, 12, 12, 24, 12, 12] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 103 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 115) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc(O)cc1) `ZINC000619974148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000619974148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000619974148 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', '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', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 21, 21, 3, 21, 21, 21, 21, 21, 21, 3, 3, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 11, 11, 7, 7, 11, 11, 3, 3, 3, 21, 21, 3, 21, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 11, 22, 11, 11] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 99 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000619974148 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000619974148 Building ZINC000620308084 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620308084 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/116 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@@H]2C)C1) `ZINC000620308084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620308084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308084 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 3, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 9, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 61 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/117 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/117' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@@H]2C)C1) `ZINC000620308084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620308084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308084 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 2, 2, 16, 16, 16, 16, 2, 2, 2, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 35 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620308084 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 Building ZINC000620308084 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620308084 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 116) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@@H]2C)C1) `ZINC000620308084.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620308084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308084 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 3, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 4, 6, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 9, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 61 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 117) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@@H]2C)C1) `ZINC000620308084.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620308084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308084 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 16, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 5, 2, 2, 2, 16, 16, 16, 16, 2, 2, 2, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 35 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620308084 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308084 Building ZINC000620308085 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620308085 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/118 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@@H](C)CC[C@@H]2C)C1) `ZINC000620308085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620308085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308085 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 53 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/119 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/119' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@@H](C)CC[C@@H]2C)C1) `ZINC000620308085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620308085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308085 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 56 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620308085 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 Building ZINC000620308085 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620308085 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 118) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@@H](C)CC[C@@H]2C)C1) `ZINC000620308085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620308085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308085 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 15, 15, 15, 15, 15, 15, 2, 2, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 6, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 53 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 119) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@@H](C)CC[C@@H]2C)C1) `ZINC000620308085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620308085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308085 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 6, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 56 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620308085 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308085 Building ZINC000620308086 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620308086 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/120 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](N2[C@H](C)CC[C@@H]2C)C1) `ZINC000620308086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620308086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308086 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](N2[C@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 7, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 54 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/121 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/121' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](N2[C@H](C)CC[C@@H]2C)C1) `ZINC000620308086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620308086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308086 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](N2[C@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 7, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 56 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620308086 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 Building ZINC000620308086 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620308086 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 120) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/120: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](N2[C@H](C)CC[C@@H]2C)C1) `ZINC000620308086.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620308086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308086 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](N2[C@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 4, 5, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 7, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 54 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 121) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/121: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](N2[C@H](C)CC[C@@H]2C)C1) `ZINC000620308086.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620308086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308086 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](N2[C@H](C)CC[C@@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 5, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 7, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 56 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620308086 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308086 Building ZINC000620308087 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620308087 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/122 `/scratch/xiaobo/281161/xco-8058088.67/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)N1CCC[C@H](N2[C@H](C)CC[C@H]2C)C1) `ZINC000620308087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620308087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308087 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 9, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/123 `/scratch/xiaobo/281161/xco-8058088.67/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)N1CCC[C@H](N2[C@H](C)CC[C@H]2C)C1) `ZINC000620308087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620308087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308087 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 4, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 3, 3, 15, 15, 11, 15, 3, 3, 3, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 65 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620308087 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 Building ZINC000620308087 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620308087 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 122) grep: /scratch/xiaobo/281161/xco-8058088.67/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)N1CCC[C@H](N2[C@H](C)CC[C@H]2C)C1) `ZINC000620308087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620308087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308087 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 20, 20, 4, 20, 20, 20, 20, 20, 20, 4, 4, 1, 1, 1, 1, 3, 5, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 9, 4, 4, 4, 20, 20, 4, 20, 4, 4, 4, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 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, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 123) grep: /scratch/xiaobo/281161/xco-8058088.67/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)N1CCC[C@H](N2[C@H](C)CC[C@H]2C)C1) `ZINC000620308087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620308087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000620308087 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](N2[C@H](C)CC[C@H]2C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 10, 5, 7, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 4, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 7, 3, 3, 3, 15, 15, 11, 15, 3, 3, 3, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 65 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620308087 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620308087 Building ZINC000620580597 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620580597 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/124 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/124' -> `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(C(=O)N2CCCC[C@H]2C)cc1C) `ZINC000620580597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620580597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000620580597 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 4, 4, 27, 27, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/125 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/125' -> `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(C(=O)N2CCCC[C@H]2C)cc1C) `ZINC000620580597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620580597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000620580597 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 3, 3, 23, 23, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620580597 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 Building ZINC000620580597 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620580597 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 124) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1C) `ZINC000620580597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620580597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000620580597 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 4, 4, 27, 27, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 104 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 125) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)cc1C) `ZINC000620580597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620580597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000620580597 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@H]2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 3, 3, 23, 23, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 3, 8, 8, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 8, 8, 8, 8] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620580597 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580597 Building ZINC000620580598 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620580598 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/126 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/126' -> `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(C(=O)N2CCCC[C@@H]2C)cc1C) `ZINC000620580598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620580598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000620580598 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 2, 21, 21, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/127 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/127' -> `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(C(=O)N2CCCC[C@@H]2C)cc1C) `ZINC000620580598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620580598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000620580598 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 4, 5, 29, 28, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620580598 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 Building ZINC000620580598 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620580598 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 126) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1C) `ZINC000620580598.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620580598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000620580598 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 2, 2, 21, 21, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 2, 7, 7, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 7, 7, 7] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 127) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)cc1C) `ZINC000620580598.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620580598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000620580598 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC[C@@H]2C)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 7, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 4, 5, 29, 28, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 3, 3, 3, 7, 7, 6, 7, 7, 3, 3, 3, 2, 6, 6, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 6, 6, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620580598 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620580598 Building ZINC000620862012 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620862012 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/128 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2n1C) `ZINC000620862012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620862012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000620862012 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 5, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 15, 15, 12, 15, 3, 3, 3, 9, 9, 9, 9, 9, 9, 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, 58, 59]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/129 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/129' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2n1C) `ZINC000620862012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620862012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000620862012 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620862012 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 Building ZINC000620862012 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620862012 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 128) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2n1C) `ZINC000620862012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620862012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000620862012 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 5, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 15, 15, 12, 15, 3, 3, 3, 9, 9, 9, 9, 9, 9, 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, 58, 59]) total number of confs: 73 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 129) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2n1C) `ZINC000620862012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620862012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000620862012 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 22, 22, 3, 22, 22, 22, 22, 22, 22, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 22, 22, 3, 22, 3, 3, 3, 8, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 71 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620862012 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862012 Building ZINC000620862013 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620862013 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/130 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2n1C) `ZINC000620862013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620862013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000620862013 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 24, 24, 10, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 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, 58, 59]) total number of confs: 82 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/131 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/131' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2n1C) `ZINC000620862013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620862013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000620862013 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 7, 14, 14, 14, 14, 14, 14, 4, 4, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 14, 14, 13, 14, 4, 4, 4, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620862013 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 Building ZINC000620862013 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000620862013 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 130) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/130: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2n1C) `ZINC000620862013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000620862013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000620862013 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 24, 24, 3, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1, 4, 4, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 24, 24, 10, 24, 3, 3, 3, 8, 8, 8, 8, 8, 8, 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, 58, 59]) total number of confs: 82 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 131) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/131: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2n1C) `ZINC000620862013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000620862013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000620862013 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1nc2ccccc2n1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 14, 14, 7, 14, 14, 14, 14, 14, 14, 4, 4, 1, 1, 1, 1, 6, 6, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 14, 14, 13, 14, 4, 4, 4, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 69 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000620862013 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000620862013 Building ZINC000071868992 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000071868992 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/132 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)sc(C)c1c1ccc(Cl)cc1Cl) `ZINC000071868992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000071868992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000071868992 none COC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)sc(C)c1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 14, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 18, 18, 11, 18, 18, 18, 18, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/133 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/133' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)sc(C)c1c1ccc(Cl)cc1Cl) `ZINC000071868992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000071868992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000071868992 none COC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)sc(C)c1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 14, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 17, 17, 10, 17, 17, 17, 17, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 17, 17, 17] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000071868992 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 Building ZINC000071868992 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000071868992 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 132) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)sc(C)c1c1ccc(Cl)cc1Cl) `ZINC000071868992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000071868992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000071868992 none COC(=O)c1c(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)sc(C)c1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 14, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 27, 11, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 11, 18, 18, 11, 18, 18, 18, 18, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 18, 18, 18] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 133) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)sc(C)c1c1ccc(Cl)cc1Cl) `ZINC000071868992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000071868992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000071868992 none COC(=O)c1c(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)sc(C)c1c1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'S.3', 'C.2', 'C.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 14, 1, 5, 1, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 27, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 17, 17, 10, 17, 17, 17, 17, 27, 27, 27, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 10, 17, 17, 17] 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000071868992 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000071868992 Building ZINC000011653548 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011653548 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/134 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(OC)cc1NC(=O)c1ccccc1) `ZINC000011653548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011653548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000011653548 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(OC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [8, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 8, 4, 4, 4, 10, 10, 10, 18, 18, 10, 18, 18, 8, 8, 8, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 8, 4, 10, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/135 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/135' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(OC)cc1NC(=O)c1ccccc1) `ZINC000011653548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011653548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000011653548 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(OC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [8, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 8, 4, 4, 4, 10, 10, 10, 18, 18, 10, 18, 18, 8, 8, 8, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 8, 8, 4, 10, 18, 18, 10, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000011653548 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 Building ZINC000011653548 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011653548 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 134) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/134: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(OC)cc1NC(=O)c1ccccc1) `ZINC000011653548.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011653548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000011653548 none COc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(OC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [8, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 4, 4, 8, 4, 4, 4, 10, 10, 10, 18, 18, 10, 18, 18, 8, 8, 8, 4, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 8, 8, 8, 4, 10, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 135) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(OC)cc1NC(=O)c1ccccc1) `ZINC000011653548.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011653548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000011653548 none COc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c(OC)cc1NC(=O)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 12, 5, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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: [8, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 4, 4, 8, 4, 4, 4, 10, 10, 10, 18, 18, 10, 18, 18, 8, 8, 8, 4, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 8, 8, 8, 4, 10, 18, 18, 10, 18, 18] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000011653548 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011653548 Building ZINC000623748321 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623748321 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/136 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCc2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)ccc21) `ZINC000623748321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623748321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000623748321 none CC(=O)N1CCCc2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/137 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/137' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCCc2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)ccc21) `ZINC000623748321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623748321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000623748321 none CC(=O)N1CCCc2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000623748321 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 Building ZINC000623748321 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000623748321 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 136) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(=O)N1CCCc2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)ccc21) `ZINC000623748321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000623748321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000623748321 none CC(=O)N1CCCc2cc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 9, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 13, 13] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 137) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(=O)N1CCCc2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)ccc21) `ZINC000623748321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000623748321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000623748321 none CC(=O)N1CCCc2cc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 10, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000623748321 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000623748321 Building ZINC000010652101 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000010652101 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/138 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/138' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000010652101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000010652101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000010652101 none CCn1c2ccccc2nc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 9, 9, 9, 9, 9, 5, 5, 5, 5, 2, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/139 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/139' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000010652101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000010652101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000010652101 none CCn1c2ccccc2nc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 8, 8, 8, 8, 8, 5, 5, 5, 5, 2, 4, 4, 4, 25, 25, 6, 25, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000010652101 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 Building ZINC000010652101 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000010652101 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 138) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCn1c2ccccc2nc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000010652101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000010652101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000010652101 none CCn1c2ccccc2nc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 26, 26, 4, 26, 26, 26, 26, 26, 26, 4, 4, 9, 9, 9, 9, 9, 5, 5, 5, 5, 2, 4, 4, 4, 26, 26, 4, 26, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 139) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCn1c2ccccc2nc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000010652101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000010652101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC000010652101 none CCn1c2ccccc2nc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 8, 8, 8, 8, 8, 5, 5, 5, 5, 2, 4, 4, 4, 25, 25, 6, 25, 4, 4, 4] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000010652101 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000010652101 Building ZINC000016233302 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016233302 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/140 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC) `ZINC000016233302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016233302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000016233302 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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: [11, 10, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 6, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/141 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/141' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC) `ZINC000016233302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016233302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000016233302 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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: [10, 10, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 6, 10, 10, 10, 10, 10, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016233302 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 Building ZINC000016233302 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016233302 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 140) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC) `ZINC000016233302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016233302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000016233302 none CCOc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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: [11, 10, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 6, 11, 11, 11, 11, 11, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 141) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC) `ZINC000016233302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016233302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000016233302 none CCOc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 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, 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: [10, 10, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 6, 10, 10, 10, 10, 10, 5, 5, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 6, 6, 6] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016233302 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016233302 Building ZINC000018004674 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000018004674 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/142 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(=O)Nc1ccc(Cl)cc1Cl)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000018004674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000018004674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000018004674 none CCCN(CC(=O)Nc1ccc(Cl)cc1Cl)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 3, 2, 3, 5, 11, 11, 11, 25, 25, 11, 18, 25, 25, 25, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 8, 8, 8, 7, 7, 5, 5, 11, 25, 25, 25, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/143 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/143' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(CC(=O)Nc1ccc(Cl)cc1Cl)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000018004674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000018004674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000018004674 none CCCN(CC(=O)Nc1ccc(Cl)cc1Cl)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 5, 11, 11, 11, 25, 25, 11, 18, 25, 25, 25, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 9, 9, 9, 9, 9, 7, 7, 5, 5, 11, 25, 25, 25, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 144 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000018004674 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 Building ZINC000018004674 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000018004674 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 142) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCCN(CC(=O)Nc1ccc(Cl)cc1Cl)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000018004674.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000018004674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000018004674 none CCCN(CC(=O)Nc1ccc(Cl)cc1Cl)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 3, 2, 3, 5, 11, 11, 11, 25, 25, 11, 18, 25, 25, 25, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 8, 8, 8, 7, 7, 5, 5, 11, 25, 25, 25, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 132 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 143) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCCN(CC(=O)Nc1ccc(Cl)cc1Cl)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000018004674.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000018004674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000018004674 none CCCN(CC(=O)Nc1ccc(Cl)cc1Cl)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 2, 3, 5, 11, 11, 11, 25, 25, 11, 18, 25, 25, 25, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 9, 9, 9, 9, 9, 7, 7, 5, 5, 11, 25, 25, 25, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 144 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000018004674 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018004674 Building ZINC000018161182 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000018161182 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/144 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1) `ZINC000018161182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000018161182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000018161182 none COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 10, 10, 10, 10, 22, 35, 50, 50, 44, 50, 50, 14, 14, 14, 10, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 10, 10, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 5, 6, 7, 8, 41, 10, 11, 12, 13, 14, 44, 16, 50, 51, 52, 22, 9, 23, 15, 42] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/145 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/145' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1) `ZINC000018161182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000018161182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000018161182 none COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 10, 10, 10, 10, 22, 35, 50, 50, 41, 50, 50, 15, 15, 15, 10, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 10, 10, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 5, 6, 7, 8, 41, 10, 11, 12, 13, 14, 44, 16, 50, 51, 52, 22, 9, 23, 15, 42] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000018161182 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 Building ZINC000018161182 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000018161182 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 144) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/144: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1) `ZINC000018161182.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000018161182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000018161182 none COc1cc(CNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 10, 10, 10, 10, 22, 35, 50, 50, 44, 50, 50, 14, 14, 14, 10, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 10, 10, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 5, 6, 7, 8, 41, 10, 11, 12, 13, 14, 44, 16, 50, 51, 52, 22, 9, 23, 15, 42] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 145) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/145: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1) `ZINC000018161182.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000018161182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000018161182 none COc1cc(CNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', '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, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 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, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 10, 10, 10, 10, 22, 35, 50, 50, 41, 50, 50, 15, 15, 15, 10, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 10, 10, 35, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 5, 6, 7, 8, 41, 10, 11, 12, 13, 14, 44, 16, 50, 51, 52, 22, 9, 23, 15, 42] set([0, 1, 2, 3, 4, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48, 49, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000018161182 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018161182 Building ZINC000018134788 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000018134788 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/146 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1) `ZINC000018134788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000018134788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000018134788 none COc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 21, 34, 45, 45, 40, 45, 45, 13, 13, 13, 6, 2, 2, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 34, 34, 45, 45, 45, 45, 45] 50 rigid atoms, others: [11, 5, 6, 7, 8, 9, 42, 43, 44, 12, 10] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/147 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/147' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1) `ZINC000018134788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000018134788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000018134788 none COc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 20, 33, 44, 44, 38, 44, 44, 13, 13, 13, 6, 2, 2, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 33, 33, 44, 44, 44, 44, 44] 50 rigid atoms, others: [11, 5, 6, 7, 8, 9, 42, 43, 44, 12, 10] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000018134788 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 Building ZINC000018134788 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000018134788 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 146) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/146: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1) `ZINC000018134788.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000018134788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000018134788 none COc1cc(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 21, 34, 45, 45, 40, 45, 45, 13, 13, 13, 6, 2, 2, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 34, 34, 45, 45, 45, 45, 45] 50 rigid atoms, others: [11, 5, 6, 7, 8, 9, 42, 43, 44, 12, 10] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 147) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1) `ZINC000018134788.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000018134788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000018134788 none COc1cc(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 20, 33, 44, 44, 38, 44, 44, 13, 13, 13, 6, 2, 2, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 33, 33, 44, 44, 44, 44, 44] 50 rigid atoms, others: [11, 5, 6, 7, 8, 9, 42, 43, 44, 12, 10] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000018134788 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000018134788 Building ZINC000024786381 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000024786381 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/148 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cn2)n1) `ZINC000024786381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000024786381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000024786381 none Cc1cc(C)n(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 2, 3, 3, 3, 12, 12, 5, 12, 3, 3, 3, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/149 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/149' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)n(c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cn2)n1) `ZINC000024786381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000024786381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000024786381 none Cc1cc(C)n(c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000024786381 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 Building ZINC000024786381 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000024786381 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 148) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(C)n(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cn2)n1) `ZINC000024786381.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000024786381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000024786381 none Cc1cc(C)n(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 7, 7, 2, 3, 3, 3, 12, 12, 5, 12, 3, 3, 3, 7] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 149) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(C)n(c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cn2)n1) `ZINC000024786381.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000024786381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000024786381 none Cc1cc(C)n(c2ccc(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)cn2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'N.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 2, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 6] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000024786381 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024786381 Building ZINC001626483055 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626483055 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/150 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001626483055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626483055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001626483055 none O=C(NCC1(c2cccc(Br)c2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 16, 26, 39, 39, 39, 39, 39, 39, 26, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 2, 13, 13, 39, 39, 39, 39, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/151 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/151' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001626483055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626483055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001626483055 none O=C(NCC1(c2cccc(Br)c2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 26, 38, 38, 38, 38, 38, 38, 26, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 2, 12, 12, 38, 38, 38, 38, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001626483055 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 Building ZINC001626483055 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001626483055 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 150) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/150: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001626483055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001626483055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001626483055 none O=C(NCC1(c2cccc(Br)c2)CCC1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 16, 26, 39, 39, 39, 39, 39, 39, 26, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 2, 13, 13, 39, 39, 39, 39, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 151) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/151: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCC1(c2cccc(Br)c2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001626483055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001626483055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001626483055 none O=C(NCC1(c2cccc(Br)c2)CCC1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 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] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 26, 38, 38, 38, 38, 38, 38, 26, 26, 26, 1, 1, 1, 7, 7, 7, 7, 7, 2, 12, 12, 38, 38, 38, 38, 26, 26, 26, 26, 26, 26, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001626483055 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001626483055 Building ZINC000029099431 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029099431 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/152 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000029099431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029099431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029099431 none COc1ccc([C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 14, 14, 7, 3, 7, 7, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 3, 3, 3, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/153 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/153' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000029099431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029099431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029099431 none COc1ccc([C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 6, 3, 6, 6, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 3, 3, 3, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029099431 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 Building ZINC000029099431 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029099431 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 152) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc([C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000029099431.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029099431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029099431 none COc1ccc([C@@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 7, 14, 14, 7, 3, 7, 7, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 3, 3, 3, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 14, 14] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 89 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 153) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc([C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000029099431.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029099431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029099431 none COc1ccc([C@@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 6, 3, 6, 6, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 3, 3, 3, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029099431 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099431 Building ZINC000029099435 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029099435 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/154 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000029099435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029099435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029099435 none COc1ccc([C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 8, 8, 6, 3, 6, 6, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 3, 3, 3, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/155 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/155' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000029099435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029099435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029099435 none COc1ccc([C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 15, 15, 7, 3, 7, 7, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 3, 3, 3, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 15, 15] 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: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029099435 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 Building ZINC000029099435 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029099435 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 154) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc([C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000029099435.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029099435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029099435 none COc1ccc([C@H](C)N(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 6, 6, 8, 8, 6, 3, 6, 6, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 3, 3, 3, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 8, 8] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 155) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc([C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1) `ZINC000029099435.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029099435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000029099435 none COc1ccc([C@H](C)N(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 15, 15, 7, 3, 7, 7, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 3, 3, 3, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 15, 15] 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: 96 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029099435 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029099435 Building ZINC000029279359 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029279359 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/156 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cc[nH]n2)cc1) `ZINC000029279359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029279359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000029279359 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cc[nH]n2)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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 1, 8, 6, 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, 7, 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, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 13, 13, 13, 13, 13, 4, 4, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 2, 4, 4, 13, 13, 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]) total number of confs: 72 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/157 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/157' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cc[nH]n2)cc1) `ZINC000029279359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029279359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000029279359 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cc[nH]n2)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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 1, 8, 6, 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, 7, 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, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 11, 11, 11, 11, 11, 4, 4, 3, 3, 3, 16, 16, 5, 16, 3, 3, 3, 2, 4, 4, 11, 11, 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]) total number of confs: 68 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029279359 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 Building ZINC000029279359 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029279359 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 156) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/156: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cc[nH]n2)cc1) `ZINC000029279359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029279359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000029279359 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2cc[nH]n2)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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 1, 8, 6, 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, 7, 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, 17, 17, 3, 17, 17, 17, 17, 17, 17, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 4, 13, 13, 13, 13, 13, 4, 4, 3, 3, 3, 17, 17, 3, 17, 3, 3, 3, 2, 4, 4, 13, 13, 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]) total number of confs: 72 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 157) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/157: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cc[nH]n2)cc1) `ZINC000029279359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029279359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000029279359 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2cc[nH]n2)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', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 1, 8, 6, 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, 7, 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, 16, 16, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 11, 11, 11, 11, 11, 4, 4, 3, 3, 3, 16, 16, 5, 16, 3, 3, 3, 2, 4, 4, 11, 11, 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]) total number of confs: 68 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029279359 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029279359 Building ZINC000029715558 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029715558 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/158 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/158' -> `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](c1ccccc1)c1ccccn1) `ZINC000029715558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029715558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000029715558 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 8, 5, 8, 8, 5, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 3, 8, 8, 5, 8, 8, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/159 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/159' -> `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](c1ccccc1)c1ccccn1) `ZINC000029715558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029715558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000029715558 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 3, 5, 5, 5, 5, 5, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029715558 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 Building ZINC000029715558 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029715558 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 158) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccccn1) `ZINC000029715558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029715558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000029715558 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 8, 8, 5, 8, 8, 5, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 3, 8, 8, 5, 8, 8, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 69 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 159) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccccn1) `ZINC000029715558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029715558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000029715558 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](c1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 3, 5, 5, 5, 5, 5, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029715558 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715558 Building ZINC000029715561 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029715561 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/160 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/160' -> `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](c1ccccc1)c1ccccn1) `ZINC000029715561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029715561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000029715561 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 4, 4, 4, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/161 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/161' -> `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](c1ccccc1)c1ccccn1) `ZINC000029715561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029715561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000029715561 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 7, 5, 7, 7, 5, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 3, 7, 7, 7, 7, 7, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029715561 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 Building ZINC000029715561 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000029715561 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 160) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccccn1) `ZINC000029715561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000029715561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000029715561 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 4, 4, 4, 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 161) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccccn1) `ZINC000029715561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000029715561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000029715561 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](c1ccccc1)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 3, 3, 3, 5, 5, 7, 7, 5, 7, 7, 5, 12, 12, 12, 12, 12, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 3, 7, 7, 7, 7, 7, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 66 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000029715561 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000029715561 Building ZINC000030118539 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000030118539 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/162 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/162' -> `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)NCc1cccc(NC(=O)C2CCC2)c1) `ZINC000030118539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000030118539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000030118539 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(NC(=O)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 14, 14, 14, 18, 18, 18, 26, 26, 26, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 7, 7, 14, 14, 14, 18, 26, 26, 26, 26, 26, 26, 26, 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, 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/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/163 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/163' -> `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)NCc1cccc(NC(=O)C2CCC2)c1) `ZINC000030118539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000030118539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000030118539 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(NC(=O)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 15, 15, 15, 21, 21, 21, 28, 28, 28, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 15, 15, 15, 21, 28, 28, 28, 28, 28, 28, 28, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000030118539 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 Building ZINC000030118539 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000030118539 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 162) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(NC(=O)C2CCC2)c1) `ZINC000030118539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000030118539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000030118539 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1cccc(NC(=O)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 14, 14, 14, 18, 18, 18, 26, 26, 26, 14, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 7, 7, 14, 14, 14, 18, 26, 26, 26, 26, 26, 26, 26, 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, 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/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 163) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(NC(=O)C2CCC2)c1) `ZINC000030118539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000030118539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000030118539 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1cccc(NC(=O)C2CCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 15, 15, 15, 21, 21, 21, 28, 28, 28, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 15, 15, 15, 21, 28, 28, 28, 28, 28, 28, 28, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000030118539 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030118539 Building ZINC000030608823 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000030608823 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/164 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/164' -> `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(n2ccnc2)cc1) `ZINC000030608823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000030608823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000030608823 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 10, 10, 10, 10, 5, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 10, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/165 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/165' -> `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(n2ccnc2)cc1) `ZINC000030608823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000030608823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000030608823 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 10, 10, 10, 5, 5, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 5, 5, 10, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000030608823 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 Building ZINC000030608823 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000030608823 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 164) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)cc1) `ZINC000030608823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000030608823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000030608823 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 2, 10, 10, 10, 10, 5, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 10, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 165) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)cc1) `ZINC000030608823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000030608823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000030608823 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2ccnc2)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', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 1, 8, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 10, 10, 10, 10, 5, 5, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 5, 5, 10, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000030608823 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030608823 Building ZINC000030862153 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000030862153 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/166 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)c(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC) `ZINC000030862153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000030862153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000030862153 none COc1cc(C)c(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 4, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 9, 8, 8, 8, 5, 5, 5, 5, 4, 4, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 9, 9, 9] 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]) total number of confs: 50 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/167 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/167' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)c(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC) `ZINC000030862153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000030862153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000030862153 none COc1cc(C)c(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 4, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 9, 8, 8, 8, 5, 5, 5, 5, 4, 4, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 9, 9, 9] 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]) total number of confs: 50 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000030862153 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 Building ZINC000030862153 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000030862153 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 166) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/166: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)c(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC) `ZINC000030862153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000030862153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000030862153 none COc1cc(C)c(CN(C)C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 4, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 9, 8, 8, 8, 5, 5, 5, 5, 4, 4, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 9, 9, 9] 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]) total number of confs: 50 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 167) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/167: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)c(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC) `ZINC000030862153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000030862153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 64 natoms 63 natoms 62 natoms 61 names: ZINC000030862153 none COc1cc(C)c(CN(C)C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 5, 8, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 4, 3, 2, 3, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 5, 5, 5, 9, 8, 8, 8, 5, 5, 5, 5, 4, 4, 3, 3, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 5, 9, 9, 9] 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]) total number of confs: 50 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000030862153 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000030862153 Building ZINC000031365046 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000031365046 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/168 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCOc1ccccc1) `ZINC000031365046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000031365046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000031365046 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCOc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 4, 5, 6, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 4, 4, 5, 5, 6, 6, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/169 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/169' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCOc1ccccc1) `ZINC000031365046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000031365046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000031365046 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCOc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 4, 5, 6, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 4, 4, 5, 5, 6, 6, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000031365046 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 Building ZINC000031365046 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000031365046 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 168) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/168: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCOc1ccccc1) `ZINC000031365046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000031365046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000031365046 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCOc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 4, 5, 6, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 4, 4, 5, 5, 6, 6, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 169) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/169: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCOc1ccccc1) `ZINC000031365046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000031365046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000031365046 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCOc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 4, 5, 6, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3, 3, 4, 4, 5, 5, 6, 6, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000031365046 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031365046 Building ZINC000031588368 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000031588368 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/170 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1)C(C)=O) `ZINC000031588368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000031588368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000031588368 none CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 2, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 12, 14, 14, 12, 12, 12, 12, 12, 10, 10, 2, 3, 3, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 14, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/171 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/171' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1)C(C)=O) `ZINC000031588368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000031588368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000031588368 none CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 10, 13, 13, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 3, 13, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000031588368 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 Building ZINC000031588368 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000031588368 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 170) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1)C(C)=O) `ZINC000031588368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000031588368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000031588368 none CCN(Cc1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 3, 2, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 12, 14, 14, 12, 12, 12, 12, 12, 10, 10, 2, 3, 3, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 14, 14, 14] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 171) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1)C(C)=O) `ZINC000031588368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000031588368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000031588368 none CCN(Cc1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1)C(C)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.2', 'C.3', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 5, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 10, 13, 13, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 3, 13, 13, 13] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000031588368 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000031588368 Building ZINC000011515887 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011515887 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/172 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/172' -> `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)NCc1ccc(OC(F)F)cc1) `ZINC000011515887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011515887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000011515887 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 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, 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, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 11, 9, 9, 23, 23, 23, 11, 11, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 2, 9, 9, 11, 11, 23, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/173 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/173' -> `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)NCc1ccc(OC(F)F)cc1) `ZINC000011515887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011515887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000011515887 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 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, 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, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 11, 9, 9, 24, 24, 24, 11, 11, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2, 2, 9, 9, 11, 11, 24, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000011515887 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 Building ZINC000011515887 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011515887 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 172) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/172: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OC(F)F)cc1) `ZINC000011515887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011515887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000011515887 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 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, 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, 7, 7, 2, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 11, 9, 9, 23, 23, 23, 11, 11, 2, 2, 2, 7, 7, 2, 7, 2, 2, 2, 2, 9, 9, 11, 11, 23, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 173) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/173: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(OC(F)F)cc1) `ZINC000011515887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011515887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000011515887 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 15, 15, 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, 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, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 11, 11, 9, 9, 24, 24, 24, 11, 11, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2, 2, 9, 9, 11, 11, 24, 11, 11] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000011515887 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011515887 Building ZINC000043730265 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043730265 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/174 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)C2CC2)c1) `ZINC000043730265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043730265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000043730265 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 10, 10, 10, 13, 13, 6, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 2, 6, 6, 6, 10, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/175 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/175' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)C2CC2)c1) `ZINC000043730265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043730265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000043730265 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 12, 12, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 6, 10, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043730265 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 Building ZINC000043730265 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043730265 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 174) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)C2CC2)c1) `ZINC000043730265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043730265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000043730265 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 10, 10, 10, 13, 13, 6, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 2, 6, 6, 6, 10, 13, 13, 13, 13, 13, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 175) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)C2CC2)c1) `ZINC000043730265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043730265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000043730265 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.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, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 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] 0 hydrogens need rotated 50 conformations in 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, 10, 10, 10, 12, 12, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 6, 10, 12, 12, 12, 12, 12, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043730265 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043730265 Building ZINC000043731306 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043731306 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/176 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@@H]2CCCO2)c1) `ZINC000043731306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043731306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000043731306 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@@H]2CCCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 11, 15, 15, 15, 15, 15, 2, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 11, 11, 15, 15, 15, 15, 15, 15, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 36, 37, 38, 43, 44, 45, 46] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/177 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/177' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@@H]2CCCO2)c1) `ZINC000043731306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043731306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000043731306 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@@H]2CCCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 14, 17, 17, 17, 17, 17, 6, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 6, 6, 6, 14, 14, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043731306 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 Building ZINC000043731306 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043731306 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 176) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/176: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@@H]2CCCO2)c1) `ZINC000043731306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043731306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000043731306 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@@H]2CCCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 11, 15, 15, 15, 15, 15, 2, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 11, 11, 15, 15, 15, 15, 15, 15, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 36, 37, 38, 43, 44, 45, 46] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 177) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/177: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@@H]2CCCO2)c1) `ZINC000043731306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043731306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000043731306 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@@H]2CCCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 13, 14, 17, 17, 17, 17, 17, 6, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 6, 6, 6, 14, 14, 17, 17, 17, 17, 17, 17, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043731306 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731306 Building ZINC000043731307 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043731307 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/178 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@H]2CCCO2)c1) `ZINC000043731307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043731307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000043731307 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@H]2CCCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 13, 14, 16, 16, 16, 16, 16, 6, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 6, 6, 6, 14, 14, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/179 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/179' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@H]2CCCO2)c1) `ZINC000043731307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043731307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000043731307 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@H]2CCCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 10, 14, 14, 14, 14, 14, 2, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 14, 14, 14, 14, 14, 14, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 36, 37, 38, 43, 44, 45, 46] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043731307 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 Building ZINC000043731307 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043731307 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 178) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@H]2CCCO2)c1) `ZINC000043731307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043731307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000043731307 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@H]2CCCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 13, 14, 16, 16, 16, 16, 16, 6, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 6, 6, 6, 14, 14, 16, 16, 16, 16, 16, 16, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 179) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@H]2CCCO2)c1) `ZINC000043731307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043731307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000043731307 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(OC[C@H]2CCCO2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 12, 5, 5, 7, 5, 5, 5, 12, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 9, 10, 14, 14, 14, 14, 14, 2, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 2, 2, 2, 10, 10, 14, 14, 14, 14, 14, 14, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 36, 37, 38, 43, 44, 45, 46] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043731307 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731307 Building ZINC000043731526 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043731526 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/180 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000043731526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043731526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043731526 none CC(=O)Nc1cccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 9, 9, 9, 9, 9, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 9, 10, 10, 10, 10, 9, 9, 9, 3, 3, 3, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 48 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/181 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/181' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000043731526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043731526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043731526 none CC(=O)Nc1cccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 2, 2, 2, 2, 8, 8, 6, 8, 2, 2, 2, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043731526 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 Building ZINC000043731526 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043731526 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 180) grep: /scratch/xiaobo/281161/xco-8058088.67/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(=O)Nc1cccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000043731526.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043731526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043731526 none CC(=O)Nc1cccc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 9, 9, 9, 9, 9, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 9, 10, 10, 10, 10, 9, 9, 9, 3, 3, 3, 2, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 48 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 181) grep: /scratch/xiaobo/281161/xco-8058088.67/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(=O)Nc1cccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000043731526.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043731526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043731526 none CC(=O)Nc1cccc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 8, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 3, 2, 2, 2, 2, 8, 8, 6, 8, 2, 2, 2, 8] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043731526 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731526 Building ZINC000043731527 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043731527 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/182 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000043731527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043731527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043731527 none CC(=O)Nc1cccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 8, 8, 8, 8, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/183 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/183' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000043731527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043731527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043731527 none CC(=O)Nc1cccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 9, 9, 9, 9, 9, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 9, 10, 10, 10, 10, 9, 9, 9, 3, 3, 3, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 52 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043731527 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 Building ZINC000043731527 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043731527 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 182) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/182: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000043731527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043731527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043731527 none CC(=O)Nc1cccc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 7, 7, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 7, 8, 8, 8, 8, 7, 7, 7, 3, 3, 3, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 7] 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]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 183) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/183: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1cccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000043731527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043731527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043731527 none CC(=O)Nc1cccc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 9, 9, 9, 9, 9, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 9, 10, 10, 10, 10, 9, 9, 9, 3, 3, 3, 2, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 9] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 52 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043731527 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043731527 Building ZINC000043756343 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043756343 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/184 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000043756343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043756343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043756343 none CCOCc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 6, 5, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 15, 15, 15, 15, 15, 14, 14, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 5, 5, 3, 5, 2, 2, 2] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/185 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/185' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000043756343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043756343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043756343 none CCOCc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 4, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 14, 14, 14, 14, 14, 13, 13, 5, 5, 5, 5, 3, 3, 1, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043756343 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 Building ZINC000043756343 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000043756343 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 184) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOCc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000043756343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000043756343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043756343 none CCOCc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 6, 5, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 15, 15, 15, 15, 15, 14, 14, 6, 6, 6, 6, 4, 4, 1, 2, 2, 2, 5, 5, 3, 5, 2, 2, 2] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 185) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOCc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000043756343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000043756343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000043756343 none CCOCc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 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, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 5, 4, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 2, 5, 5, 5, 5, 5, 5, 2, 2, 14, 14, 14, 14, 14, 13, 13, 5, 5, 5, 5, 3, 3, 1, 2, 2, 2, 5, 5, 2, 5, 2, 2, 2] 50 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000043756343 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000043756343 Building ZINC000045899273 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000045899273 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/186 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/186' -> `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(c2nc3ccccc3[nH]2)CC1) `ZINC000045899273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000045899273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000045899273 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3ccccc3[nH]2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 1, 4, 6, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 2, 17, 17, 2, 17, 2, 2, 2, 7, 7, 7, 7, 7, 14, 14, 14, 14, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 61 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/187 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/187' -> `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(c2nc3ccccc3[nH]2)CC1) `ZINC000045899273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000045899273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000045899273 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3ccccc3[nH]2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 2, 2, 2, 13, 13, 3, 13, 2, 2, 2, 8, 8, 8, 8, 8, 16, 16, 16, 16, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000045899273 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 Building ZINC000045899273 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000045899273 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 186) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3ccccc3[nH]2)CC1) `ZINC000045899273.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000045899273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000045899273 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2nc3ccccc3[nH]2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 17, 17, 2, 17, 17, 17, 17, 17, 17, 2, 2, 1, 1, 1, 1, 4, 6, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 2, 17, 17, 2, 17, 2, 2, 2, 7, 7, 7, 7, 7, 14, 14, 14, 14, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 61 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 187) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3ccccc3[nH]2)CC1) `ZINC000045899273.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000045899273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000045899273 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2nc3ccccc3[nH]2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 13, 13, 2, 13, 13, 13, 13, 13, 13, 2, 2, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 2, 2, 2, 13, 13, 3, 13, 2, 2, 2, 8, 8, 8, 8, 8, 16, 16, 16, 16, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000045899273 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000045899273 Building ZINC000499385235 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499385235 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/188 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000499385235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499385235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000499385235 none CCN(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 13, 24, 24, 24, 20, 24, 24, 24, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 4, 4, 4, 4, 4, 13, 13, 24, 24, 24, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/189 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/189' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000499385235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499385235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000499385235 none CCN(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 12, 22, 22, 22, 17, 22, 22, 22, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 4, 4, 4, 4, 4, 12, 12, 22, 22, 22, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3] 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]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499385235 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 Building ZINC000499385235 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499385235 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 188) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000499385235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499385235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000499385235 none CCN(Cc1cc(Br)ccc1F)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 13, 24, 24, 24, 20, 24, 24, 24, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 2, 2, 4, 4, 4, 4, 4, 13, 13, 24, 24, 24, 2, 2, 2, 6, 6, 4, 6, 6, 2, 2, 2] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 112 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 189) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000499385235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499385235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000499385235 none CCN(Cc1cc(Br)ccc1F)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 17, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 2, 3, 12, 22, 22, 22, 17, 22, 22, 22, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 4, 4, 4, 4, 4, 12, 12, 22, 22, 22, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3] 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]) total number of confs: 110 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499385235 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499385235 Building ZINC000046778568 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046778568 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/190 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(COCc2ccccc2)cc1) `ZINC000046778568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046778568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000046778568 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 8, 8, 24, 24, 46, 50, 50, 50, 50, 50, 13, 13, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 13, 13, 24, 24, 46, 46, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/191 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/191' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(COCc2ccccc2)cc1) `ZINC000046778568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046778568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000046778568 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 12, 12, 8, 8, 22, 22, 45, 49, 49, 46, 49, 49, 12, 12, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 8, 8, 12, 12, 22, 22, 45, 45, 49, 49, 49, 49, 49, 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]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000046778568 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 Building ZINC000046778568 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046778568 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 190) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(COCc2ccccc2)cc1) `ZINC000046778568.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046778568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000046778568 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc(COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 1, 1, 1, 1, 2, 2, 2, 8, 13, 13, 8, 8, 24, 24, 46, 50, 50, 50, 50, 50, 13, 13, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 13, 13, 24, 24, 46, 46, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 245 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 191) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(COCc2ccccc2)cc1) `ZINC000046778568.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046778568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000046778568 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc(COCc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 12, 12, 8, 8, 22, 22, 45, 49, 49, 46, 49, 49, 12, 12, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 8, 8, 12, 12, 22, 22, 45, 45, 49, 49, 49, 49, 49, 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]) total number of confs: 256 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000046778568 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046778568 Building ZINC000046797760 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046797760 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/192 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/192' -> `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(=O)c2ccc(CC(C)C)cc2)CC1) `ZINC000046797760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046797760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000046797760 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(CC(C)C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 12, 12, 21, 21, 12, 12, 40, 40, 40, 21, 21, 4, 4, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 21, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 193 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/193 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/193' -> `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(=O)c2ccc(CC(C)C)cc2)CC1) `ZINC000046797760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046797760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000046797760 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(CC(C)C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 12, 12, 21, 21, 14, 21, 37, 37, 37, 21, 21, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 21, 21, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000046797760 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 Building ZINC000046797760 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046797760 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 192) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/192: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(CC(C)C)cc2)CC1) `ZINC000046797760.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046797760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000046797760 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(CC(C)C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 12, 12, 21, 21, 12, 12, 40, 40, 40, 21, 21, 4, 4, 2, 2, 2, 5, 5, 4, 5, 5, 2, 2, 2, 4, 4, 4, 4, 4, 21, 21, 40, 40, 40, 40, 40, 40, 40, 40, 40, 21, 21, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 193 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 193) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/193: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(CC(C)C)cc2)CC1) `ZINC000046797760.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046797760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000046797760 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(CC(C)C)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 4, 4, 12, 12, 21, 21, 14, 21, 37, 37, 37, 21, 21, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 21, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 21, 21, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000046797760 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046797760 Building ZINC000046836683 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046836683 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/194 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(NC(=O)C2CC2)cc1) `ZINC000046836683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046836683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000046836683 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 6, 6, 4, 5, 12, 12, 12, 12, 12, 6, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 4, 4, 4, 6, 6, 12, 12, 12, 12, 12, 12, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/195 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/195' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(NC(=O)C2CC2)cc1) `ZINC000046836683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046836683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000046836683 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 6, 6, 4, 4, 15, 15, 15, 16, 16, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 4, 6, 6, 15, 16, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000046836683 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 Building ZINC000046836683 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046836683 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 194) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(NC(=O)C2CC2)cc1) `ZINC000046836683.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046836683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000046836683 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 6, 6, 4, 5, 12, 12, 12, 12, 12, 6, 6, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 4, 4, 4, 6, 6, 12, 12, 12, 12, 12, 12, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 195) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(NC(=O)C2CC2)cc1) `ZINC000046836683.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046836683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000046836683 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H](C)c1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 6, 6, 4, 4, 15, 15, 15, 16, 16, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 4, 4, 4, 6, 6, 15, 16, 16, 16, 16, 16, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000046836683 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836683 Building ZINC000046836685 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046836685 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/196 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(NC(=O)C2CC2)cc1) `ZINC000046836685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046836685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000046836685 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 5, 7, 15, 15, 15, 17, 17, 7, 7, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 7, 7, 15, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/197 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/197' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(NC(=O)C2CC2)cc1) `ZINC000046836685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046836685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000046836685 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 6, 6, 4, 6, 10, 10, 10, 10, 10, 6, 6, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 4, 4, 4, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000046836685 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 Building ZINC000046836685 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000046836685 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 196) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/196: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(NC(=O)C2CC2)cc1) `ZINC000046836685.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000046836685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000046836685 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 7, 7, 5, 7, 15, 15, 15, 17, 17, 7, 7, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 7, 7, 15, 17, 17, 17, 17, 17, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 197) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/197: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(NC(=O)C2CC2)cc1) `ZINC000046836685.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000046836685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000046836685 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H](C)c1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 6, 6, 4, 6, 10, 10, 10, 10, 10, 6, 6, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 4, 4, 4, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000046836685 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000046836685 Building ZINC000106153851 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106153851 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/198 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/198' -> `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)Nc1nc2ccc(OCC(F)(F)F)cc2s1) `ZINC000106153851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106153851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000106153851 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(OCC(F)(F)F)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 24, 27, 27, 27, 27, 5, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 5, 5, 27, 27, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/199 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/199' -> `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)Nc1nc2ccc(OCC(F)(F)F)cc2s1) `ZINC000106153851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106153851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000106153851 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(OCC(F)(F)F)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 5, 5, 5, 26, 27, 27, 27, 27, 5, 5, 5, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 5, 5, 27, 27, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000106153851 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 Building ZINC000106153851 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000106153851 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 198) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(OCC(F)(F)F)cc2s1) `ZINC000106153851.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000106153851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000106153851 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(OCC(F)(F)F)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 24, 27, 27, 27, 27, 5, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 5, 5, 27, 27, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 199) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(OCC(F)(F)F)cc2s1) `ZINC000106153851.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000106153851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000106153851 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(OCC(F)(F)F)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 5, 5, 5, 26, 27, 27, 27, 27, 5, 5, 5, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 5, 5, 27, 27, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000106153851 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000106153851 Building ZINC000108160459 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000108160459 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/200 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/200' -> `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)NCc1ccc([N@]2CC[C@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/201 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/201' -> `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)NCc1ccc([N@]2CC[C@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/202 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/202' -> `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)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/203 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/203' -> `3.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)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 7, 7, 7, 7, 2, 2, 2, 1, 5, 5, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108160459 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 Building ZINC000108160459 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000108160459 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 200) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 201) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 202) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 203) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 7, 7, 7, 7, 2, 2, 2, 1, 5, 5, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108160459 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 Building ZINC000108160459 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000108160459 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 200) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 201) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 202) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 203) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 7, 7, 7, 7, 2, 2, 2, 1, 5, 5, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108160459 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 Building ZINC000108160459 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000108160459 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 200) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 201) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 202) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/202: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 1, 1, 1, 4, 4, 1, 4, 1, 1, 1, 1, 5, 5, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 37, 38, 39, 44, 45, 46, 47] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 203) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1) `ZINC000108160459.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000108160459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000108160459 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccc([N@]2CC[C@@H](C)CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 7, 5, 5, 5, 8, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 9, 9, 2, 2, 2, 7, 7, 7, 7, 2, 2, 2, 1, 5, 5, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9] 50 rigid atoms, others: [47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108160459 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108160459 Building ZINC000108327672 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108327672 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/204 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccn2)cc1) `ZINC000108327672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108327672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108327672 none CCOc1ccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 22, 22, 31, 31, 22, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 11, 11, 11, 31, 31, 50, 50, 50, 50, 50, 31, 31, 11, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 11, 11, 31, 31] 50 rigid atoms, others: [48, 45, 54, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 22, 55, 56, 47, 28, 29, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/205 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/205' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccn2)cc1) `ZINC000108327672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108327672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108327672 none CCOc1ccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 30, 30, 30, 21, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 10, 10, 10, 30, 30, 50, 50, 50, 50, 50, 30, 30, 10, 4, 4, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 10, 10, 30, 30] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 45, 46, 47, 48, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 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/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108327672 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 Building ZINC000108327672 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108327672 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 204) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOc1ccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccn2)cc1) `ZINC000108327672.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108327672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108327672 none CCOc1ccc(Oc2cc(CNC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 22, 22, 31, 31, 22, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 11, 11, 11, 31, 31, 50, 50, 50, 50, 50, 31, 31, 11, 4, 4, 1, 1, 1, 1, 2, 2, 2, 2, 2, 1, 1, 1, 11, 11, 31, 31] 50 rigid atoms, others: [48, 45, 54, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 46, 22, 55, 56, 47, 28, 29, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 57, 58, 59, 60]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 205) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOc1ccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccn2)cc1) `ZINC000108327672.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108327672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108327672 none CCOc1ccc(Oc2cc(CNC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4ccccc4)c3C)ccn2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 30, 30, 30, 21, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 10, 10, 10, 30, 30, 50, 50, 50, 50, 50, 30, 30, 10, 4, 4, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 10, 10, 30, 30] 50 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 45, 46, 47, 48, 54, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 49, 50, 51, 52, 53, 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/281161/xco-8058088.67/working/building/ZINC000108327672 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108327672 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327672 Building ZINC000108327721 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108327721 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/206 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(F)c2)c1) `ZINC000108327721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108327721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000108327721 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 8, 8, 8, 28, 28, 28, 28, 28, 28, 6, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 6, 6, 6, 8, 28, 28, 28, 28, 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]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/207 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/207' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(F)c2)c1) `ZINC000108327721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108327721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000108327721 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 31, 31, 31, 31, 31, 31, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 6, 6, 6, 9, 31, 31, 31, 31, 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]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108327721 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 Building ZINC000108327721 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108327721 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 206) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(F)c2)c1) `ZINC000108327721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108327721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000108327721 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 8, 8, 8, 28, 28, 28, 28, 28, 28, 6, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 3, 6, 6, 6, 8, 28, 28, 28, 28, 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]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 207) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(F)c2)c1) `ZINC000108327721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108327721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000108327721 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)Nc2cccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 9, 9, 9, 31, 31, 31, 31, 31, 31, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 6, 6, 6, 9, 31, 31, 31, 31, 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]) total number of confs: 70 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108327721 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108327721 Building ZINC000108365896 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108365896 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/208 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000108365896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108365896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108365896 none COc1cccc(C[C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 4, 3, 3, 3, 3, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/209 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/209' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000108365896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108365896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108365896 none COc1cccc(C[C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 5, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 9, 10, 10, 10, 9, 9, 9, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 9] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108365896 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 Building ZINC000108365896 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108365896 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 208) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cccc(C[C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000108365896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108365896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108365896 none COc1cccc(C[C@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 4, 3, 3, 3, 3, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 7] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 209) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cccc(C[C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000108365896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108365896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108365896 none COc1cccc(C[C@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 5, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 4, 10, 10, 10, 10, 10, 10, 2, 2, 9, 10, 10, 10, 9, 9, 9, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2, 9] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108365896 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365896 Building ZINC000108365899 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108365899 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/210 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000108365899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108365899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108365899 none COc1cccc(C[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 5, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 9, 10, 10, 10, 9, 9, 9, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 9] 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/211 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/211' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(C[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000108365899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108365899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108365899 none COc1cccc(C[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 5, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 8, 8, 8, 8, 8, 8, 8, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108365899 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 Building ZINC000108365899 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108365899 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 210) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cccc(C[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000108365899.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108365899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108365899 none COc1cccc(C[C@@H]2CCCN2C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 9, 9, 9, 9, 5, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 9, 10, 10, 10, 9, 9, 9, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 10, 10, 10, 10, 2, 2, 2, 9] 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]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 211) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cccc(C[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000108365899.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108365899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000108365899 none COc1cccc(C[C@@H]2CCCN2C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 5, 3, 3, 3, 3, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 8, 8, 8, 8, 8, 8, 8, 5, 5, 3, 3, 3, 3, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 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, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 53 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108365899 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108365899 Building ZINC000108707115 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108707115 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/212 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/212' -> `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)NCc1ccccc1N1CCCC1) `ZINC000108707115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108707115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000108707115 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 15, 12, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/213 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/213' -> `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)NCc1ccccc1N1CCCC1) `ZINC000108707115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108707115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000108707115 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 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, 58]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108707115 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 Building ZINC000108707115 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000108707115 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 212) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1N1CCCC1) `ZINC000108707115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000108707115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000108707115 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 15, 15, 12, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 213) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1N1CCCC1) `ZINC000108707115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000108707115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000108707115 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1N1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 14, 14, 10, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 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, 58]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000108707115 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000108707115 Building ZINC000508902321 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508902321 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/214 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000508902321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508902321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000508902321 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 9, 9, 7, 9, 9, 4, 12, 12, 12, 26, 26, 12, 12, 26, 26, 12, 12, 4, 4, 4, 4, 4, 4, 6, 6, 9, 9, 9, 9, 9, 26, 26, 26, 26, 12, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/215 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/215' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000508902321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508902321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000508902321 none Cn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 4, 5, 7, 10, 10, 8, 10, 10, 5, 13, 13, 13, 25, 25, 13, 17, 25, 25, 13, 13, 4, 4, 4, 4, 4, 4, 7, 7, 10, 10, 10, 10, 10, 25, 25, 25, 25, 13, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000508902321 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 Building ZINC000508902321 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000508902321 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 214) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000508902321.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000508902321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000508902321 none Cn1cc([C@@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 9, 9, 7, 9, 9, 4, 12, 12, 12, 26, 26, 12, 12, 26, 26, 12, 12, 4, 4, 4, 4, 4, 4, 6, 6, 9, 9, 9, 9, 9, 26, 26, 26, 26, 12, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 215) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccc(Br)cc3)cs2)cn1) `ZINC000508902321.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000508902321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC000508902321 none Cn1cc([C@]([O-])([SiH3])C(=O)N(Cc2ccccc2)c2nc(c3ccc(Br)cc3)cs2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', '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, 8, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 4, 4, 5, 7, 10, 10, 8, 10, 10, 5, 13, 13, 13, 25, 25, 13, 17, 25, 25, 13, 13, 4, 4, 4, 4, 4, 4, 7, 7, 10, 10, 10, 10, 10, 25, 25, 25, 25, 13, 4] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000508902321 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000508902321 Building ZINC000012737871 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012737871 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/216 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1Cl) `ZINC000012737871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012737871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000012737871 none CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 9, 9, 9, 9, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/217 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/217' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1Cl) `ZINC000012737871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012737871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000012737871 none CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 9, 9, 9, 9, 4, 4, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000012737871 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 Building ZINC000012737871 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012737871 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 216) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/216: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1Cl) `ZINC000012737871.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012737871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000012737871 none CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 9, 9, 9, 9, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 217) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/217: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1Cl) `ZINC000012737871.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012737871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC000012737871 none CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 16, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 4, 9, 9, 9, 9, 4, 4, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 4] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000012737871 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012737871 Building ZINC000012827195 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012827195 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/218 `/scratch/xiaobo/281161/xco-8058088.67/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)NCc1ccccc1OC(F)F) `ZINC000012827195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012827195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000012827195 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 11, 11, 11, 11, 11, 13, 13, 13, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 10, 10, 11, 11, 11, 11, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/219 `/scratch/xiaobo/281161/xco-8058088.67/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)NCc1ccccc1OC(F)F) `ZINC000012827195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012827195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000012827195 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 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: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 12, 12, 12, 12, 12, 14, 14, 14, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 2, 9, 9, 12, 12, 12, 12, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000012827195 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 Building ZINC000012827195 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000012827195 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 218) grep: /scratch/xiaobo/281161/xco-8058088.67/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)NCc1ccccc1OC(F)F) `ZINC000012827195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000012827195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000012827195 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 11, 11, 11, 11, 11, 13, 13, 13, 3, 3, 3, 10, 10, 3, 10, 3, 3, 3, 2, 10, 10, 11, 11, 11, 11, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 219) grep: /scratch/xiaobo/281161/xco-8058088.67/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)NCc1ccccc1OC(F)F) `ZINC000012827195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000012827195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000012827195 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1OC(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 5, 15, 15, 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, 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: [2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 2, 2, 2, 9, 12, 12, 12, 12, 12, 12, 14, 14, 14, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 2, 9, 9, 12, 12, 12, 12, 14] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000012827195 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000012827195 Building ZINC000624835869 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000624835869 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/220 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/220' -> `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)n(c2cc(C(F)(F)F)ccc2Cl)n1) `ZINC000624835869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000624835869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000624835869 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n(c2cc(C(F)(F)F)ccc2Cl)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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 11, 11, 26, 26, 26, 26, 26, 26, 19, 26, 26, 26, 11, 11, 11, 11, 11, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 26, 22, 26] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/221 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/221' -> `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)n(c2cc(C(F)(F)F)ccc2Cl)n1) `ZINC000624835869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000624835869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000624835869 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n(c2cc(C(F)(F)F)ccc2Cl)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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 10, 10, 26, 26, 26, 26, 26, 26, 10, 26, 26, 26, 10, 10, 10, 10, 10, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 26, 22, 26] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000624835869 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 Building ZINC000624835869 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000624835869 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 220) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n(c2cc(C(F)(F)F)ccc2Cl)n1) `ZINC000624835869.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000624835869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000624835869 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n(c2cc(C(F)(F)F)ccc2Cl)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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 8, 8, 8, 6, 11, 11, 26, 26, 26, 26, 26, 26, 19, 26, 26, 26, 11, 11, 11, 11, 11, 5, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 26, 22, 26] 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]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 221) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n(c2cc(C(F)(F)F)ccc2Cl)n1) `ZINC000624835869.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000624835869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000624835869 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2cnn(C(C)(C)C)c2)n(c2cc(C(F)(F)F)ccc2Cl)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.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 5, 5, 5, 1, 8, 1, 1, 1, 5, 15, 15, 15, 1, 1, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 7, 7, 7, 6, 10, 10, 26, 26, 26, 26, 26, 26, 10, 26, 26, 26, 10, 10, 10, 10, 10, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 26, 22, 26] 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]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000624835869 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000624835869 Building ZINC000499468890 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499468890 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/222 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCSCC1) `ZINC000499468890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499468890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499468890 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 19, 34, 34, 33, 34, 34, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 5, 12, 12, 12, 34, 34, 34, 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]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/223 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/223' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCSCC1) `ZINC000499468890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499468890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499468890 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 5, 12, 12, 19, 36, 36, 35, 36, 34, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 5, 12, 12, 12, 36, 36, 36, 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]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499468890 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 Building ZINC000499468890 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499468890 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 222) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCSCC1) `ZINC000499468890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499468890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499468890 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 4, 9, 9, 3, 3, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 19, 34, 34, 33, 34, 34, 3, 3, 3, 9, 9, 6, 9, 9, 3, 3, 3, 5, 12, 12, 12, 34, 34, 34, 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]) total number of confs: 88 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 223) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCSCC1) `ZINC000499468890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499468890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000499468890 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(Cl)ccc1N1CCSCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 8, 5, 5, 14, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 5, 12, 12, 19, 36, 36, 35, 36, 34, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 3, 5, 12, 12, 12, 36, 36, 36, 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]) total number of confs: 125 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499468890 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499468890 Building ZINC000110613347 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110613347 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/224 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1) `ZINC000110613347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110613347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000110613347 none Cc1csc(CCCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1 NO_LONG_NAME dock atom types: ['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', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 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, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 9, 7, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 15, 15, 15, 15, 15, 10, 10, 9, 9, 9, 9, 6, 6, 1, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 44, 13, 12, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/225 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/225' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1csc(CCCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1) `ZINC000110613347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110613347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000110613347 none Cc1csc(CCCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1 NO_LONG_NAME dock atom types: ['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', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 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, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 11, 10, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 16, 16, 16, 16, 16, 11, 11, 10, 10, 10, 10, 6, 6, 1, 2, 2, 2, 6, 6, 4, 6, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 44, 13, 12, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000110613347 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 Building ZINC000110613347 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000110613347 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 224) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1csc(CCCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1) `ZINC000110613347.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000110613347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000110613347 none Cc1csc(CCCCNC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1 NO_LONG_NAME dock atom types: ['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', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 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, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 9, 7, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 15, 15, 15, 15, 15, 10, 10, 9, 9, 9, 9, 6, 6, 1, 2, 2, 2, 6, 6, 2, 6, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 44, 13, 12, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 225) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1csc(CCCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1) `ZINC000110613347.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000110613347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000110613347 none Cc1csc(CCCCNC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n1 NO_LONG_NAME dock atom types: ['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', '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', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 14, 1, 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, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 11, 10, 8, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 6, 6, 2, 6, 6, 6, 6, 6, 6, 2, 2, 16, 16, 16, 16, 16, 11, 11, 10, 10, 10, 10, 6, 6, 1, 2, 2, 2, 6, 6, 4, 6, 2, 2, 2] 50 rigid atoms, others: [8, 9, 10, 11, 44, 13, 12, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000110613347 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000110613347 Building ZINC000499525943 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499525943 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/226 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCCC2)c1C) `ZINC000499525943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499525943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000499525943 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCCC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/227 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/227' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCCC2)c1C) `ZINC000499525943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499525943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000499525943 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCCC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499525943 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 Building ZINC000499525943 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499525943 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 226) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/226: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCCC2)c1C) `ZINC000499525943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499525943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000499525943 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCCC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 9, 9, 9, 9, 9, 9, 6, 6, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 6, 6, 6, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 227) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/227: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCCC2)c1C) `ZINC000499525943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499525943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000499525943 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCCC2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499525943 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499525943 Building ZINC000499665029 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499665029 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/228 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCc3ccccc32)c1) `ZINC000499665029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499665029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000499665029 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCc3ccccc32)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', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 16, 37, 37, 41, 41, 41, 41, 41, 41, 41, 41, 14, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 4, 4, 14, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/229 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/229' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCc3ccccc32)c1) `ZINC000499665029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499665029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000499665029 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCc3ccccc32)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', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 16, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 14, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 14, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499665029 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 Building ZINC000499665029 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000499665029 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 228) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCc3ccccc32)c1) `ZINC000499665029.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000499665029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000499665029 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCc3ccccc32)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', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 16, 37, 37, 41, 41, 41, 41, 41, 41, 41, 41, 14, 4, 4, 4, 6, 6, 4, 6, 6, 4, 4, 4, 4, 14, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 229) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCc3ccccc32)c1) `ZINC000499665029.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000499665029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000499665029 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(=O)N2CCc3ccccc32)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', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 16, 34, 34, 38, 38, 38, 38, 38, 38, 38, 38, 14, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 14, 14, 14, 38, 38, 38, 38, 38, 38, 38, 38, 14] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 103 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000499665029 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000499665029 Building ZINC000115980821 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115980821 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/230 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/230' -> `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)NCc1ccccc1n1ccnc1C) `ZINC000115980821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115980821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000115980821 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1n1ccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 11, 12, 12, 12, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 12, 12, 12, 12, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/231 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/231' -> `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)NCc1ccccc1n1ccnc1C) `ZINC000115980821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115980821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000115980821 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1n1ccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 12, 13, 13, 13, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000115980821 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 Building ZINC000115980821 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000115980821 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 230) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1n1ccnc1C) `ZINC000115980821.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000115980821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000115980821 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1n1ccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 12, 12, 11, 12, 12, 12, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 6, 6, 12, 12, 12, 12, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 231) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1n1ccnc1C) `ZINC000115980821.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000115980821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000115980821 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1n1ccnc1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 13, 13, 12, 13, 13, 13, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 13, 13, 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, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000115980821 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000115980821 Building ZINC000625047720 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000625047720 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/232 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/232' -> `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)CCCc1cc(c2ccc(F)cc2)no1) `ZINC000625047720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000625047720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000625047720 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccc(F)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 6, 8, 13, 29, 29, 29, 39, 39, 37, 37, 39, 39, 29, 29, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 4, 4, 4, 6, 6, 9, 9, 13, 12, 29, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/233 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/233' -> `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)CCCc1cc(c2ccc(F)cc2)no1) `ZINC000625047720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000625047720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000625047720 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccc(F)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 6, 8, 13, 29, 29, 29, 39, 39, 38, 39, 39, 39, 29, 29, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 6, 6, 9, 9, 13, 12, 29, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000625047720 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 Building ZINC000625047720 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000625047720 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 232) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccc(F)cc2)no1) `ZINC000625047720.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000625047720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000625047720 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccc(F)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 5, 5, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 6, 8, 13, 29, 29, 29, 39, 39, 37, 37, 39, 39, 29, 29, 2, 2, 2, 5, 5, 2, 5, 5, 2, 2, 2, 4, 4, 4, 6, 6, 9, 9, 13, 12, 29, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 121 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 233) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccc(F)cc2)no1) `ZINC000625047720.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000625047720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000625047720 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCCc1cc(c2ccc(F)cc2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 15, 1, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 6, 8, 13, 29, 29, 29, 39, 39, 38, 39, 39, 39, 29, 29, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 6, 6, 9, 9, 13, 12, 29, 39, 39, 39, 39] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000625047720 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000625047720 Building ZINC000303049867 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303049867 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/234 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/234' -> `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)Nc1cnn(c2ccccc2)c1) `ZINC000303049867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303049867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303049867 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 15, 15, 15, 15, 4, 4, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 15, 15, 4, 15, 4, 4, 4, 4, 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/235 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/235' -> `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)Nc1cnn(c2ccccc2)c1) `ZINC000303049867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303049867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303049867 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 13, 13, 12, 13, 13, 12, 4, 4, 4, 17, 17, 6, 17, 4, 4, 4, 4, 12, 13, 13, 12, 13, 13, 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]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303049867 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 Building ZINC000303049867 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303049867 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 234) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2)c1) `ZINC000303049867.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303049867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303049867 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 15, 15, 4, 15, 15, 15, 15, 15, 15, 4, 4, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 15, 15, 4, 15, 4, 4, 4, 4, 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]) total number of confs: 54 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 235) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2)c1) `ZINC000303049867.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303049867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000303049867 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnn(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 8, 1, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 17, 17, 4, 17, 17, 17, 17, 17, 17, 4, 4, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 13, 13, 12, 13, 13, 12, 4, 4, 4, 17, 17, 6, 17, 4, 4, 4, 4, 12, 13, 13, 12, 13, 13, 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]) total number of confs: 70 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303049867 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303049867 Building ZINC000014361779 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000014361779 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/236 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/236' -> `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(NC(=O)C2CC2)cc1) `ZINC000014361779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000014361779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000014361779 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 10, 10, 10, 12, 12, 3, 3, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 3, 3, 10, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/237 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/237' -> `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(NC(=O)C2CC2)cc1) `ZINC000014361779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000014361779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000014361779 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 12, 12, 12, 14, 14, 5, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 12, 14, 14, 14, 14, 14, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000014361779 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 Building ZINC000014361779 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000014361779 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 236) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)C2CC2)cc1) `ZINC000014361779.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000014361779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000014361779 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 10, 10, 10, 12, 12, 3, 3, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 3, 3, 10, 12, 12, 12, 12, 12, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 67 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 237) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)C2CC2)cc1) `ZINC000014361779.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000014361779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000014361779 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 2, 4, 12, 12, 12, 14, 14, 5, 5, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 12, 14, 14, 14, 14, 14, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000014361779 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000014361779 Building ZINC000016206639 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016206639 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/238 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000016206639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016206639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000016206639 none CCN(CC)C(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4] 50 rigid atoms, others: [16, 11, 12, 13, 14, 15, 48, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/239 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/239' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000016206639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016206639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000016206639 none CCN(CC)C(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4] 50 rigid atoms, others: [16, 11, 12, 13, 14, 15, 48, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016206639 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 Building ZINC000016206639 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016206639 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 238) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(CC)C(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000016206639.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016206639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000016206639 none CCN(CC)C(=O)c1cccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4] 50 rigid atoms, others: [16, 11, 12, 13, 14, 15, 48, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 239) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(CC)C(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1) `ZINC000016206639.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016206639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC000016206639 none CCN(CC)C(=O)c1cccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 4, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 4, 1, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 4] 50 rigid atoms, others: [16, 11, 12, 13, 14, 15, 48, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016206639 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016206639 Building ZINC000016235174 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016235174 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/240 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C2CC2)cc1) `ZINC000016235174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016235174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000016235174 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 9, 9, 6, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 3, 4, 4, 9, 9, 9, 9, 9, 9, 9, 6, 6, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/241 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/241' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C2CC2)cc1) `ZINC000016235174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016235174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000016235174 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 10, 6, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 3, 5, 5, 10, 10, 10, 10, 10, 10, 10, 6, 6, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 5, 5, 5, 5, 5, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016235174 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 Building ZINC000016235174 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016235174 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 240) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/240: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C2CC2)cc1) `ZINC000016235174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016235174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000016235174 none COc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 9, 9, 6, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 15, 15, 2, 15, 15, 15, 15, 15, 15, 2, 2, 3, 4, 4, 9, 9, 9, 9, 9, 9, 9, 6, 6, 2, 2, 2, 15, 15, 2, 15, 2, 2, 2, 4, 4, 4, 4, 4, 9, 9] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 79 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 241) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C2CC2)cc1) `ZINC000016235174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016235174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC000016235174 none COc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)C2CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', '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', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 10, 10, 6, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 14, 14, 2, 14, 14, 14, 14, 14, 14, 2, 2, 3, 5, 5, 10, 10, 10, 10, 10, 10, 10, 6, 6, 2, 2, 2, 14, 14, 2, 14, 2, 2, 2, 5, 5, 5, 5, 5, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016235174 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016235174 Building ZINC000016260264 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016260264 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/242 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc2c(c1)OCCO2) `ZINC000016260264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016260264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016260264 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 5, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 15, 15, 5, 15, 3, 3, 3, 5, 5, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/243 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/243' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc2c(c1)OCCO2) `ZINC000016260264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016260264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016260264 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 5, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 53 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016260264 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 Building ZINC000016260264 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016260264 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 242) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc2c(c1)OCCO2) `ZINC000016260264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016260264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016260264 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 15, 15, 5, 15, 15, 15, 15, 15, 15, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 15, 15, 5, 15, 3, 3, 3, 5, 5, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 57 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 243) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc2c(c1)OCCO2) `ZINC000016260264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016260264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016260264 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H]1c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 3, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 5, 5, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 53 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016260264 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260264 Building ZINC000016260265 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016260265 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/244 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc2c(c1)OCCO2) `ZINC000016260265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016260265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016260265 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 18, 18, 18, 18, 3, 3, 3, 5, 5, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 41 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/245 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/245' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc2c(c1)OCCO2) `ZINC000016260265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016260265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016260265 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 9, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 12, 14, 3, 3, 3, 5, 5, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 55 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016260265 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 Building ZINC000016260265 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016260265 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 244) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc2c(c1)OCCO2) `ZINC000016260265.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016260265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016260265 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 18, 18, 18, 18, 3, 3, 3, 5, 5, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 41 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 245) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc2c(c1)OCCO2) `ZINC000016260265.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016260265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016260265 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]1c1ccc2c(c1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 12, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 14, 14, 9, 14, 14, 14, 14, 14, 14, 3, 3, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 14, 14, 12, 14, 3, 3, 3, 5, 5, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 55 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016260265 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016260265 Building ZINC000016263291 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016263291 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/246 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/246' -> `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)Nc1cnc2c(cnn2C(C)C)c1) `ZINC000016263291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016263291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016263291 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc2c(cnn2C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 8, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 8, 8, 12, 12, 12, 12, 12, 12, 12, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/247 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/247' -> `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)Nc1cnc2c(cnn2C(C)C)c1) `ZINC000016263291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016263291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016263291 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc2c(cnn2C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 7, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016263291 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 Building ZINC000016263291 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016263291 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 246) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/246: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc2c(cnn2C(C)C)c1) `ZINC000016263291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016263291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016263291 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc2c(cnn2C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 8, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 8, 8, 12, 12, 12, 12, 12, 12, 12, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 247) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/247: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc2c(cnn2C(C)C)c1) `ZINC000016263291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016263291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016263291 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc2c(cnn2C(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', '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', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 8, 8, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 7, 3, 3, 3, 13, 13, 5, 13, 3, 3, 3, 2, 7, 7, 11, 11, 11, 11, 11, 11, 11, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016263291 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263291 Building ZINC000016263409 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016263409 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/248 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/248' -> `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)CCOc1cccc(C)c1) `ZINC000016263409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016263409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016263409 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 7, 11, 11, 7, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 1, 1, 1, 2, 2, 3, 3, 11, 11, 7, 11, 11, 11, 11] 50 rigid atoms, others: [43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/249 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/249' -> `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)CCOc1cccc(C)c1) `ZINC000016263409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016263409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016263409 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 11, 11, 11, 11, 11, 2, 2, 2, 9, 9, 5, 9, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 49 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016263409 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 Building ZINC000016263409 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000016263409 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 248) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1cccc(C)c1) `ZINC000016263409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000016263409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016263409 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(C)CCOc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 7, 11, 11, 7, 11, 11, 11, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 1, 1, 1, 2, 2, 3, 3, 11, 11, 7, 11, 11, 11, 11] 50 rigid atoms, others: [43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 59 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 249) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1cccc(C)c1) `ZINC000016263409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000016263409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000016263409 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C)CCOc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 1, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 9, 9, 9, 9, 9, 9, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 11, 11, 11, 11, 11, 2, 2, 2, 9, 9, 5, 9, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11] 50 rigid atoms, others: [43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 49 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000016263409 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000016263409 Building ZINC000509302393 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000509302393 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/250 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)OCCO2) `ZINC000509302393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000509302393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000509302393 none CSc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 5, 5, 12, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/251 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/251' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)OCCO2) `ZINC000509302393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000509302393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000509302393 none CSc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 5, 5, 12, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000509302393 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 Building ZINC000509302393 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000509302393 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 250) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CSc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)OCCO2) `ZINC000509302393.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000509302393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000509302393 none CSc1cc2c(cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 5, 5, 12, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 251) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CSc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)OCCO2) `ZINC000509302393.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000509302393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000509302393 none CSc1cc2c(cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c3cccc(C(F)(F)F)c3)c1C)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 12, 5, 5, 12, 7, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 9, 9, 2, 9, 9, 9, 9, 9, 9, 2, 2, 4, 4, 4, 4, 10, 10, 10, 4, 4, 2, 2, 2, 2, 9, 9, 2, 9, 2, 2, 2, 4, 4, 4, 4] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000509302393 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509302393 Building ZINC000594570516 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000594570516 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/252 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc(Cc2ccc(C)cc2)s1) `ZINC000594570516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594570516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594570516 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc(Cc2ccc(C)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 1, 5, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/253 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/253' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc(Cc2ccc(C)cc2)s1) `ZINC000594570516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594570516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594570516 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc(Cc2ccc(C)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 1, 5, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000594570516 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 Building ZINC000594570516 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000594570516 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 252) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc(Cc2ccc(C)cc2)s1) `ZINC000594570516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000594570516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594570516 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nnc(Cc2ccc(C)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 1, 5, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 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]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 253) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/253: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc(Cc2ccc(C)cc2)s1) `ZINC000594570516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000594570516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000594570516 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nnc(Cc2ccc(C)cc2)s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom 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, 1, 5, 1, 1, 1, 1, 5, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 13, 3, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000594570516 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000594570516 Building ZINC000509437244 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000509437244 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/254 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/254' -> `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]1CC[N@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/255 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/255' -> `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]1CC[N@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/256 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/256' -> `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)N[C@H]1CC[N@@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/257 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/257' -> `3.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]1CC[N@@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000509437244 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 Building ZINC000509437244 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000509437244 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 254) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 255) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 256) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[N@@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 257) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[N@@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000509437244 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 Building ZINC000509437244 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000509437244 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 254) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 255) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 256) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[N@@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 257) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[N@@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000509437244 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 Building ZINC000509437244 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC000509437244 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 254) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 8, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 8, 8, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 255) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 256) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[N@@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `2.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 7, 7, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 257) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/257: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CC[N@@](CCc2ccccc2)CC1) `ZINC000509437244.mol2' -> `3.mol2' `temp.mol2' -> `ZINC000509437244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC000509437244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1CC[N@@](CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 10, 5, 5, 1, 1, 1, 1, 1, 1, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 7, 7, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000509437244 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509437244 Building ZINC000509447767 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000509447767 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/258 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/258' -> `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)NCC1(c2ccccc2)CCOCC1) `ZINC000509447767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000509447767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000509447767 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccccc2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 1, 1, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 9, 9, 11, 11, 11, 11, 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, 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/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/259 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/259' -> `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)NCC1(c2ccccc2)CCOCC1) `ZINC000509447767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000509447767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000509447767 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccccc2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 1, 1, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000509447767 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767 Building ZINC000509447767 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000509447767 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 258) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccccc2)CCOCC1) `ZINC000509447767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000509447767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000509447767 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCC1(c2ccccc2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 1, 1, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 6, 12, 3, 3, 3, 2, 9, 9, 11, 11, 11, 11, 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, 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/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 259) grep: /scratch/xiaobo/281161/xco-8058088.67/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(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccccc2)CCOCC1) `ZINC000509447767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000509447767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000509447767 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCC1(c2ccccc2)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', '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, 1, 1, 1, 1, 1, 1, 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, 7] dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/281161/xco-8058088.67/working/building/ZINC000509447767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000509447767 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000509447767 Building ZINC000017824492 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017824492 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/260 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)Nc2ccccc2)C1) `ZINC000017824492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017824492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000017824492 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 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, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 19, 19, 2, 19, 19, 19, 19, 19, 19, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 14, 14, 7, 14, 14, 2, 2, 2, 2, 19, 19, 2, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 14, 14, 7, 14, 14, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/261 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/261' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)Nc2ccccc2)C1) `ZINC000017824492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017824492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000017824492 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 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, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 3, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 22, 22, 15, 22, 22, 3, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 3, 3, 3, 3, 3, 3, 15, 22, 22, 15, 22, 22, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000017824492 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 Building ZINC000017824492 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017824492 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 260) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)Nc2ccccc2)C1) `ZINC000017824492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017824492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000017824492 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 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, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 19, 19, 2, 19, 19, 19, 19, 19, 19, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 7, 7, 7, 14, 14, 7, 14, 14, 2, 2, 2, 2, 19, 19, 2, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 7, 14, 14, 7, 14, 14, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 87 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 261) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)Nc2ccccc2)C1) `ZINC000017824492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017824492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000017824492 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@@H](C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 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, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 3, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 15, 22, 22, 15, 22, 22, 3, 2, 2, 2, 11, 11, 3, 11, 2, 2, 2, 3, 3, 3, 3, 3, 3, 15, 22, 22, 15, 22, 22, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000017824492 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824492 Building ZINC000017824495 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017824495 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/262 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)Nc2ccccc2)C1) `ZINC000017824495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017824495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000017824495 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 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, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 18, 18, 17, 18, 18, 2, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 82 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/263 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/263' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)Nc2ccccc2)C1) `ZINC000017824495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017824495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000017824495 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 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, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 19, 19, 2, 19, 19, 19, 19, 19, 19, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 16, 16, 13, 16, 16, 3, 2, 2, 2, 19, 19, 2, 19, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 16, 16, 16, 16, 16, 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]) total number of confs: 91 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000017824495 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 Building ZINC000017824495 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000017824495 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 262) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)Nc2ccccc2)C1) `ZINC000017824495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000017824495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000017824495 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 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, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 18, 18, 17, 18, 18, 2, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 2, 2, 2, 2, 2, 2, 11, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 82 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 263) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)Nc2ccccc2)C1) `ZINC000017824495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000017824495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000017824495 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H](C(=O)Nc2ccccc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 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, 7] dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 19, 19, 2, 19, 19, 19, 19, 19, 19, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 8, 16, 16, 13, 16, 16, 3, 2, 2, 2, 19, 19, 2, 19, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 16, 16, 16, 16, 16, 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]) total number of confs: 91 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000017824495 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000017824495 Building ZINC000727324255 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727324255 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/264 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/264' -> `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(NC(=O)CN2CCCCCCC2)cc1) `ZINC000727324255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727324255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000727324255 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CN2CCCCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 10, 10, 10, 37, 42, 42, 42, 42, 42, 42, 42, 4, 4, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 4, 4, 10, 35, 35, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/265 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/265' -> `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(NC(=O)CN2CCCCCCC2)cc1) `ZINC000727324255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727324255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000727324255 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CN2CCCCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 4, 11, 11, 11, 40, 48, 48, 48, 48, 48, 48, 48, 5, 5, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 5, 5, 11, 37, 37, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727324255 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 Building ZINC000727324255 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727324255 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 264) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CN2CCCCCCC2)cc1) `ZINC000727324255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727324255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000727324255 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CN2CCCCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 10, 10, 10, 37, 42, 42, 42, 42, 42, 42, 42, 4, 4, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 4, 4, 10, 35, 35, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 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, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 265) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CN2CCCCCCC2)cc1) `ZINC000727324255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727324255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 72 natoms 71 natoms 70 natoms 69 names: ZINC000727324255 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)CN2CCCCCCC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.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, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 4, 11, 11, 11, 40, 48, 48, 48, 48, 48, 48, 48, 5, 5, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 5, 5, 11, 37, 37, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 5] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727324255 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727324255 Building ZINC000727334881 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727334881 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/266 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F) `ZINC000727334881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727334881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000727334881 none COC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 10, 10, 10, 9, 3, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 3, 3] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/267 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/267' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F) `ZINC000727334881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727334881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000727334881 none COC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 10, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 10, 10, 10, 9, 3, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727334881 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 Building ZINC000727334881 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727334881 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 266) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F) `ZINC000727334881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727334881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000727334881 none COC(=O)Nc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 10, 10, 10, 9, 3, 1, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 3, 3] 50 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 267) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F) `ZINC000727334881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727334881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC000727334881 none COC(=O)Nc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 15, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 9, 10, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 3, 3, 3, 3, 10, 10, 10, 9, 3, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 3, 3] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727334881 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727334881 Building ZINC000727764395 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727764395 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/268 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@@H](O)c2ccccc2)c1) `ZINC000727764395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727764395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727764395 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@@H](O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 2, 9, 9, 15, 22, 39, 39, 39, 39, 39, 39, 39, 39, 9, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 9, 9, 2, 15, 15, 22, 22, 117, 39, 39, 39, 39, 39, 9] 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: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/269 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/269' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@@H](O)c2ccccc2)c1) `ZINC000727764395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727764395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727764395 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@@H](O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 11, 11, 3, 11, 11, 17, 27, 45, 45, 45, 46, 46, 45, 46, 46, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 3, 17, 17, 27, 27, 135, 46, 46, 45, 46, 46, 11] 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: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727764395 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 Building ZINC000727764395 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727764395 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 268) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@@H](O)c2ccccc2)c1) `ZINC000727764395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727764395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727764395 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@@H](O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 9, 2, 9, 9, 15, 22, 39, 39, 39, 39, 39, 39, 39, 39, 9, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 3, 2, 9, 9, 2, 15, 15, 22, 22, 117, 39, 39, 39, 39, 39, 9] 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: 314 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 269) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@@H](O)c2ccccc2)c1) `ZINC000727764395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727764395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727764395 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@@H](O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 11, 11, 3, 11, 11, 17, 27, 45, 45, 45, 46, 46, 45, 46, 46, 11, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 3, 11, 11, 3, 17, 17, 27, 27, 135, 46, 46, 45, 46, 46, 11] 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: 371 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727764395 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764395 Building ZINC000727764396 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727764396 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/270 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/270' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@H](O)c2ccccc2)c1) `ZINC000727764396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727764396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727764396 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@H](O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 10, 16, 24, 41, 41, 41, 41, 41, 41, 41, 41, 10, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 10, 10, 9, 16, 16, 24, 24, 123, 41, 41, 41, 41, 41, 10] 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: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/271 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/271' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@H](O)c2ccccc2)c1) `ZINC000727764396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727764396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727764396 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@H](O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 16, 24, 42, 42, 42, 43, 43, 43, 43, 43, 10, 3, 3, 3, 5, 5, 4, 5, 5, 3, 3, 3, 3, 10, 10, 10, 16, 16, 24, 24, 126, 43, 43, 43, 43, 43, 10] 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: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727764396 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 Building ZINC000727764396 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727764396 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 270) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@H](O)c2ccccc2)c1) `ZINC000727764396.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727764396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727764396 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@H](O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 3, 10, 10, 16, 24, 41, 41, 41, 41, 41, 41, 41, 41, 10, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 10, 10, 9, 16, 16, 24, 24, 123, 41, 41, 41, 41, 41, 10] 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: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 271) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@H](O)c2ccccc2)c1) `ZINC000727764396.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727764396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727764396 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(CC[C@H](O)c2ccccc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 3, 5, 5, 3, 3, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 16, 24, 42, 42, 42, 43, 43, 43, 43, 43, 10, 3, 3, 3, 5, 5, 4, 5, 5, 3, 3, 3, 3, 10, 10, 10, 16, 16, 24, 24, 126, 43, 43, 43, 43, 43, 10] 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: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727764396 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727764396 Building ZINC000727763864 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727763864 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/272 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/272' -> `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(CC[C@@H](O)c2ccccc2)cc1) `ZINC000727763864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727763864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727763864 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@@H](O)c2ccccc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 10, 17, 37, 37, 37, 39, 39, 37, 39, 39, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 10, 10, 17, 17, 111, 39, 39, 37, 39, 39, 5, 5] 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: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/273 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/273' -> `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(CC[C@@H](O)c2ccccc2)cc1) `ZINC000727763864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727763864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727763864 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@@H](O)c2ccccc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 3, 11, 18, 40, 40, 40, 42, 42, 40, 42, 42, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 11, 11, 18, 18, 120, 42, 42, 40, 42, 42, 6, 6] 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: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727763864 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 Building ZINC000727763864 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727763864 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 272) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@@H](O)c2ccccc2)cc1) `ZINC000727763864.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727763864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727763864 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@@H](O)c2ccccc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 10, 17, 37, 37, 37, 39, 39, 37, 39, 39, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 10, 10, 17, 17, 111, 39, 39, 37, 39, 39, 5, 5] 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: 310 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 273) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@@H](O)c2ccccc2)cc1) `ZINC000727763864.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727763864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727763864 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@@H](O)c2ccccc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 3, 11, 18, 40, 40, 40, 42, 42, 40, 42, 42, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 11, 11, 18, 18, 120, 42, 42, 40, 42, 42, 6, 6] 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: 337 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727763864 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763864 Building ZINC000727763865 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727763865 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/274 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/274' -> `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(CC[C@H](O)c2ccccc2)cc1) `ZINC000727763865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727763865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727763865 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@H](O)c2ccccc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 10, 17, 38, 38, 38, 40, 40, 38, 40, 40, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 10, 10, 17, 17, 114, 40, 40, 38, 40, 40, 5, 5] 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: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/275 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/275' -> `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(CC[C@H](O)c2ccccc2)cc1) `ZINC000727763865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727763865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727763865 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@H](O)c2ccccc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 11, 19, 40, 40, 40, 42, 42, 40, 42, 42, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 11, 11, 19, 19, 120, 42, 42, 40, 42, 42, 6, 6] 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: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727763865 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 Building ZINC000727763865 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000727763865 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 274) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/274: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@H](O)c2ccccc2)cc1) `ZINC000727763865.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000727763865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727763865 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@H](O)c2ccccc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 4, 5, 10, 17, 38, 38, 38, 40, 40, 38, 40, 40, 5, 5, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 10, 10, 17, 17, 114, 40, 40, 38, 40, 40, 5, 5] 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: 316 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 275) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/275: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@H](O)c2ccccc2)cc1) `ZINC000727763865.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000727763865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000727763865 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(CC[C@H](O)c2ccccc2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 5, 7, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 4, 11, 19, 40, 40, 40, 42, 42, 40, 42, 42, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 11, 11, 19, 19, 120, 42, 42, 40, 42, 42, 6, 6] 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: 342 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000727763865 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000727763865 Building ZINC000023955228 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000023955228 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/276 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OC)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000023955228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000023955228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000023955228 none CCN(Cc1ccc(OC)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 4, 4, 4, 4, 8, 4, 4, 9, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 9, 9, 9, 4, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [1, 2, 3, 14, 15, 16, 17, 18] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/277 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/277' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OC)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000023955228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000023955228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000023955228 none CCN(Cc1ccc(OC)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 4, 4, 4, 4, 8, 4, 4, 9, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 9, 9, 9, 4, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [1, 2, 3, 14, 15, 16, 17, 18] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000023955228 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 Building ZINC000023955228 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000023955228 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 276) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/276: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OC)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000023955228.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000023955228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000023955228 none CCN(Cc1ccc(OC)c(OC)c1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 4, 4, 4, 4, 8, 4, 4, 9, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 9, 9, 9, 4, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [1, 2, 3, 14, 15, 16, 17, 18] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 277) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OC)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000023955228.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000023955228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000023955228 none CCN(Cc1ccc(OC)c(OC)c1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 4, 4, 4, 4, 8, 4, 4, 9, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 9, 9, 9, 4, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [1, 2, 3, 14, 15, 16, 17, 18] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000023955228 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000023955228 Building ZINC000024652152 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000024652152 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/278 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/278' -> `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)NCc1ccccc1CN1CCCC1) `ZINC000024652152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000024652152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000024652152 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 11, 10, 11, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 11, 11, 7, 11, 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, 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/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/279 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/279' -> `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)NCc1ccccc1CN1CCCC1) `ZINC000024652152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000024652152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000024652152 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 10, 10, 7, 10, 9, 10, 14, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 10, 10, 7, 10, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000024652152 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152 Building ZINC000024652152 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000024652152 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 278) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCC1) `ZINC000024652152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000024652152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000024652152 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 11, 11, 11, 11, 10, 11, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 11, 11, 7, 11, 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, 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/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 279) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCC1) `ZINC000024652152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000024652152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000024652152 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCc1ccccc1CN1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 10, 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, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 2, 2, 7, 10, 10, 7, 10, 9, 10, 14, 15, 15, 15, 15, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 7, 7, 10, 10, 7, 10, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/281161/xco-8058088.67/working/building/ZINC000024652152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000024652152 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000024652152 Building ZINC000730836485 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000730836485 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/280 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/280' -> `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](O)c1cccc(C(F)(F)F)c1) `ZINC000730836485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000730836485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000730836485 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 6, 6, 24, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/281 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/281' -> `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](O)c1cccc(C(F)(F)F)c1) `ZINC000730836485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000730836485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000730836485 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 8, 12, 3, 3, 3, 2, 5, 5, 24, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000730836485 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 Building ZINC000730836485 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000730836485 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 280) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/280: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c1cccc(C(F)(F)F)c1) `ZINC000730836485.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000730836485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000730836485 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H](O)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 6, 6, 24, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 281) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/281: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)c1cccc(C(F)(F)F)c1) `ZINC000730836485.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000730836485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000730836485 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H](O)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 8, 12, 3, 3, 3, 2, 5, 5, 24, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000730836485 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836485 Building ZINC000730836486 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000730836486 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/282 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/282' -> `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](O)c1cccc(C(F)(F)F)c1) `ZINC000730836486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000730836486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000730836486 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 12, 12, 11, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 24, 12, 12, 11, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/283 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/283' -> `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](O)c1cccc(C(F)(F)F)c1) `ZINC000730836486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000730836486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000730836486 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 3, 7, 7, 27, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000730836486 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 Building ZINC000730836486 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000730836486 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 282) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/282: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)c1cccc(C(F)(F)F)c1) `ZINC000730836486.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000730836486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000730836486 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H](O)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 8, 8, 8, 12, 12, 11, 12, 12, 12, 12, 12, 12, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 5, 5, 24, 12, 12, 11, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 283) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/283: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)c1cccc(C(F)(F)F)c1) `ZINC000730836486.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000730836486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000730836486 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H](O)c1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 12, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 3, 3, 3, 11, 11, 3, 11, 11, 11, 11, 11, 11, 3, 3, 1, 1, 1, 1, 3, 3, 3, 7, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 3, 7, 7, 27, 12, 12, 12, 12] 150 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000730836486 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000730836486 Building ZINC000731023133 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731023133 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/284 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/284' -> `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)N1CCCc2cc(CNC(=O)OC(C)(C)C)ccc21) `ZINC000731023133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731023133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000731023133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(CNC(=O)OC(C)(C)C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 27, 49, 49, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 66, 67] set([5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/285 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/285' -> `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)N1CCCc2cc(CNC(=O)OC(C)(C)C)ccc21) `ZINC000731023133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731023133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000731023133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(CNC(=O)OC(C)(C)C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 66, 67] set([5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000731023133 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 Building ZINC000731023133 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000731023133 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 284) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(CNC(=O)OC(C)(C)C)ccc21) `ZINC000731023133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000731023133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000731023133 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCc2cc(CNC(=O)OC(C)(C)C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 27, 49, 49, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 66, 67] set([5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 285) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(CNC(=O)OC(C)(C)C)ccc21) `ZINC000731023133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000731023133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC000731023133 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCc2cc(CNC(=O)OC(C)(C)C)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 28, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 2, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 66, 67] set([5, 6, 7, 8, 9, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41, 42, 43, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000731023133 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000731023133 Building ZINC000742523915 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000742523915 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/286 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/286' -> `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)Nc1ccccc1CN(C)C(=O)OC(C)(C)C) `ZINC000742523915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000742523915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000742523915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 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] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 6, 20, 26, 26, 43, 43, 48, 48, 48, 48, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 6, 6, 20, 20, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 182 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/287 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/287' -> `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)Nc1ccccc1CN(C)C(=O)OC(C)(C)C) `ZINC000742523915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000742523915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000742523915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 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] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 2, 6, 6, 6, 18, 27, 27, 42, 42, 47, 47, 47, 47, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 6, 6, 2, 6, 18, 18, 27, 27, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000742523915 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 Building ZINC000742523915 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000742523915 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 286) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)OC(C)(C)C) `ZINC000742523915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000742523915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000742523915 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 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] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 6, 20, 26, 26, 43, 43, 48, 48, 48, 48, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 6, 6, 20, 20, 26, 26, 26, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 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: 182 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 287) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)OC(C)(C)C) `ZINC000742523915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000742523915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000742523915 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1CN(C)C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 5, 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] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 2, 6, 6, 6, 18, 27, 27, 42, 42, 47, 47, 47, 47, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 2, 6, 6, 2, 6, 18, 18, 27, 27, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000742523915 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000742523915 Building ZINC000745069090 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000745069090 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/288 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C)c1C(=O)NCCc1ccccc1) `ZINC000745069090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000745069090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000745069090 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C)c1C(=O)NCCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 28, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 8, 28, 28, 37, 37, 37, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/289 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/289' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C)c1C(=O)NCCc1ccccc1) `ZINC000745069090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000745069090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000745069090 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C)c1C(=O)NCCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 5, 6, 6, 6, 6, 8, 8, 8, 28, 38, 38, 38, 38, 38, 38, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 8, 28, 28, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000745069090 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 Building ZINC000745069090 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000745069090 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 288) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C)c1C(=O)NCCc1ccccc1) `ZINC000745069090.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000745069090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000745069090 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C)c1C(=O)NCCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 28, 37, 37, 37, 37, 37, 37, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 8, 28, 28, 37, 37, 37, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 289) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C)c1C(=O)NCCc1ccccc1) `ZINC000745069090.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000745069090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC000745069090 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C)c1C(=O)NCCc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 5, 6, 6, 6, 6, 8, 8, 8, 28, 38, 38, 38, 38, 38, 38, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 3, 2, 6, 6, 6, 6, 6, 6, 8, 28, 28, 38, 38, 38, 38, 38, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000745069090 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745069090 Building ZINC000745406751 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000745406751 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/290 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/290' -> `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)Nc1ccccc1C(=O)Nc1ccc(Cl)cn1) `ZINC000745406751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000745406751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000745406751 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 33, 31, 31, 37, 37, 37, 37, 37, 37, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 4, 10, 10, 10, 10, 33, 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, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/291 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/291' -> `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)Nc1ccccc1C(=O)Nc1ccc(Cl)cn1) `ZINC000745406751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000745406751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000745406751 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 32, 30, 30, 37, 37, 37, 37, 37, 37, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 4, 10, 10, 10, 10, 32, 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, 51, 52, 53]) total number of confs: 118 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000745406751 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 Building ZINC000745406751 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000745406751 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 290) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1ccc(Cl)cn1) `ZINC000745406751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000745406751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000745406751 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 33, 31, 31, 37, 37, 37, 37, 37, 37, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 4, 10, 10, 10, 10, 33, 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, 51, 52, 53]) total number of confs: 112 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 291) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1ccc(Cl)cn1) `ZINC000745406751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000745406751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000745406751 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1ccc(Cl)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 16, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 32, 30, 30, 37, 37, 37, 37, 37, 37, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 4, 10, 10, 10, 10, 32, 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, 51, 52, 53]) total number of confs: 118 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000745406751 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000745406751 Building ZINC000105222359 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105222359 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/292 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000105222359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105222359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000105222359 none CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 5, 5, 5, 5, 26, 26, 5, 26, 26, 26, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 6, 4, 4, 2, 2, 26, 26, 9, 26, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [2, 3, 4, 17, 18, 19, 20, 21] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/293 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/293' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000105222359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105222359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000105222359 none CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 5, 5, 5, 5, 25, 25, 5, 25, 25, 25, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 6, 4, 4, 2, 2, 25, 25, 8, 25, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [2, 3, 4, 17, 18, 19, 20, 21] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000105222359 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 Building ZINC000105222359 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105222359 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 292) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/292: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000105222359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105222359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000105222359 none CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 5, 5, 5, 5, 26, 26, 5, 26, 26, 26, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 6, 4, 4, 2, 2, 26, 26, 9, 26, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [2, 3, 4, 17, 18, 19, 20, 21] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 293) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/293: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000105222359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105222359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC000105222359 none CCCN(Cc1nnc(c2ccccc2Cl)o1)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 16, 12, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 2, 5, 5, 5, 5, 25, 25, 5, 25, 25, 25, 5, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 6, 4, 4, 2, 2, 25, 25, 8, 25, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [2, 3, 4, 17, 18, 19, 20, 21] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000105222359 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105222359 Building ZINC000105234192 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105234192 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/294 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/294' -> `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)Nc1ccnn1Cc1cccc(Cl)c1Cl) `ZINC000105234192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105234192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105234192 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 5, 13, 13, 13, 13, 13, 32, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 13, 13, 32, 32, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/295 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/295' -> `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)Nc1ccnn1Cc1cccc(Cl)c1Cl) `ZINC000105234192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105234192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105234192 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 5, 13, 13, 13, 13, 13, 32, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 5, 13, 13, 32, 32, 43, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000105234192 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 Building ZINC000105234192 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105234192 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 294) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/294: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl) `ZINC000105234192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105234192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105234192 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 5, 13, 13, 13, 13, 13, 32, 42, 42, 42, 42, 42, 42, 42, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 3, 5, 13, 13, 32, 32, 42, 42, 42] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 295) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl) `ZINC000105234192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105234192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105234192 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccnn1Cc1cccc(Cl)c1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 8, 5, 1, 1, 1, 1, 1, 16, 1, 16, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 7, 7, 3, 7, 7, 3, 3, 1, 1, 1, 1, 2, 2, 5, 13, 13, 13, 13, 13, 32, 43, 43, 43, 43, 43, 43, 43, 3, 3, 3, 7, 7, 5, 7, 7, 3, 3, 3, 5, 13, 13, 32, 32, 43, 43, 43] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000105234192 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105234192 Building ZINC000812039395 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000812039395 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/296 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/296' -> `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(c2nnc3n2CCCCCC3)cc1) `ZINC000812039395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000812039395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000812039395 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCCCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/297 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/297' -> `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(c2nnc3n2CCCCCC3)cc1) `ZINC000812039395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000812039395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000812039395 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCCCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 26, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000812039395 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 Building ZINC000812039395 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000812039395 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 296) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCCCC3)cc1) `ZINC000812039395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000812039395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000812039395 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCCCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 24, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 297) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/297: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCCCC3)cc1) `ZINC000812039395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000812039395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC000812039395 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(c2nnc3n2CCCCCC3)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 8, 1, 8, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 6, 26, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 6, 6] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 91 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000812039395 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000812039395 Building ZINC000821933855 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000821933855 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/298 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@H](C)c1ccccc1) `ZINC000821933855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000821933855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000821933855 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 12, 12, 25, 25, 25, 37, 37, 25, 37, 37, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 3, 5, 5, 5, 5, 13, 25, 25, 25, 37, 37, 25, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 177 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/299 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/299' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@H](C)c1ccccc1) `ZINC000821933855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000821933855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000821933855 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 9, 9, 9, 23, 23, 23, 33, 33, 23, 33, 33, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 5, 5, 9, 23, 23, 23, 33, 33, 23, 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 157 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000821933855 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 Building ZINC000821933855 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000821933855 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 298) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/298: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@H](C)c1ccccc1) `ZINC000821933855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000821933855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000821933855 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 12, 12, 25, 25, 25, 37, 37, 25, 37, 37, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 3, 5, 5, 5, 5, 13, 25, 25, 25, 37, 37, 25, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 177 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 299) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/299: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@H](C)c1ccccc1) `ZINC000821933855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000821933855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000821933855 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 9, 9, 9, 23, 23, 23, 33, 33, 23, 33, 33, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 2, 5, 5, 5, 5, 9, 23, 23, 23, 33, 33, 23, 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, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 157 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000821933855 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933855 Building ZINC000821933856 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000821933856 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/300 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/300' -> `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)Nc1ccccc1C(=O)N[C@@H](C)c1ccccc1) `ZINC000821933856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000821933856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000821933856 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 9, 9, 9, 22, 22, 22, 32, 32, 22, 32, 32, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 5, 5, 5, 5, 9, 22, 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]) total number of confs: 150 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/301 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/301' -> `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)Nc1ccccc1C(=O)N[C@@H](C)c1ccccc1) `ZINC000821933856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000821933856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000821933856 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 6, 6, 6, 6, 6, 6, 14, 13, 13, 27, 26, 26, 38, 38, 26, 38, 38, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 6, 6, 6, 6, 14, 26, 26, 26, 38, 38, 26, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 176 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000821933856 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 Building ZINC000821933856 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000821933856 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 300) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@@H](C)c1ccccc1) `ZINC000821933856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000821933856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000821933856 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 5, 6, 6, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 9, 9, 9, 22, 22, 22, 32, 32, 22, 32, 32, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 2, 5, 5, 5, 5, 9, 22, 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]) total number of confs: 150 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 301) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@@H](C)c1ccccc1) `ZINC000821933856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000821933856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000821933856 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)N[C@@H](C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 6, 6, 6, 6, 6, 6, 14, 13, 13, 27, 26, 26, 38, 38, 26, 38, 38, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 6, 6, 6, 6, 14, 26, 26, 26, 38, 38, 26, 38, 38] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 176 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000821933856 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933856 Building ZINC000821933886 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000821933886 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/302 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC(=O)c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000821933886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000821933886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000821933886 none COc1cccc(NC(=O)c2ccccc2NC(=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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 6, 6, 3, 6, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 23, 31, 31, 31, 23, 23, 23, 6, 3, 3, 3, 3, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 23] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/303 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/303' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(NC(=O)c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000821933886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000821933886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000821933886 none COc1cccc(NC(=O)c2ccccc2NC(=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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 24, 24, 24, 24, 6, 6, 3, 6, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 24, 32, 32, 32, 24, 24, 24, 6, 3, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 24] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 68 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000821933886 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 Building ZINC000821933886 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000821933886 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 302) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cccc(NC(=O)c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000821933886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000821933886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000821933886 none COc1cccc(NC(=O)c2ccccc2NC(=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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens 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, 23, 23, 23, 23, 23, 6, 6, 3, 6, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 3, 5, 5, 3, 3, 23, 31, 31, 31, 23, 23, 23, 6, 3, 3, 3, 3, 2, 3, 3, 3, 5, 5, 5, 5, 5, 3, 3, 3, 23] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 71 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 303) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cccc(NC(=O)c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)c1) `ZINC000821933886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000821933886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000821933886 none COc1cccc(NC(=O)c2ccccc2NC(=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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 8, 1, 11, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 24, 24, 24, 24, 6, 6, 3, 6, 3, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 24, 32, 32, 32, 24, 24, 24, 6, 3, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 24] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 68 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000821933886 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000821933886 Building ZINC000823619619 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000823619619 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/304 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/304' -> `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)Nc1ccccc1C(=O)NCC(C)C) `ZINC000823619619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000823619619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000823619619 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 10, 10, 10, 15, 16, 16, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 2, 6, 6, 6, 6, 10, 15, 15, 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, 58, 59]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/305 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/305' -> `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)Nc1ccccc1C(=O)NCC(C)C) `ZINC000823619619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000823619619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000823619619 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 6, 6, 6, 11, 11, 11, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 67 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000823619619 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 Building ZINC000823619619 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000823619619 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 304) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCC(C)C) `ZINC000823619619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000823619619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000823619619 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 10, 10, 10, 15, 16, 16, 2, 2, 2, 10, 10, 3, 10, 2, 2, 2, 2, 6, 6, 6, 6, 10, 15, 15, 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, 58, 59]) total number of confs: 81 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 305) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCC(C)C) `ZINC000823619619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000823619619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000823619619 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 5, 6, 6, 6, 11, 11, 11, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 2, 5, 5, 5, 5, 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, 58, 59]) total number of confs: 67 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000823619619 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000823619619 Building ZINC000824091667 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000824091667 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/306 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000824091667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000824091667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000824091667 none COc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/307 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/307' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000824091667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000824091667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000824091667 none COc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000824091667 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 Building ZINC000824091667 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000824091667 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 306) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000824091667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000824091667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000824091667 none COc1ccc2c(c1)CCCN2C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 20, 20, 2, 20, 2, 2, 2] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 66 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 307) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000824091667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000824091667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000824091667 none COc1ccc2c(c1)CCCN2C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 3, 6, 1, 1, 1, 2, 2, 2, 2, 2, 20, 20, 2, 20, 20, 20, 20, 20, 20, 2, 2, 10, 10, 10, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 2, 2, 20, 20, 4, 20, 2, 2, 2] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 70 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000824091667 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000824091667 Building ZINC000825221747 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000825221747 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/308 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/308' -> `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(N2CCCC2)cc1) `ZINC000825221747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000825221747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000825221747 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 4, 4, 9, 9, 9, 9, 9, 9, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 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]) total number of confs: 94 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/309 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/309' -> `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(N2CCCC2)cc1) `ZINC000825221747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000825221747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000825221747 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 7, 10, 11, 11, 11, 11, 10, 10, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 4, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 91 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000825221747 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 Building ZINC000825221747 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000825221747 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 308) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)cc1) `ZINC000825221747.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000825221747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000825221747 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 9, 9, 4, 4, 9, 9, 9, 9, 9, 9, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 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]) total number of confs: 94 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 309) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)cc1) `ZINC000825221747.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000825221747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000825221747 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2)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', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 4, 4, 4, 10, 10, 7, 10, 11, 11, 11, 11, 10, 10, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 4, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 91 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000825221747 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000825221747 Building ZINC001143959993 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959993 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/310 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1nc(Sc1cc(Cl)cc(Cl)c1)n2CCCNC(C)C) `ZINC001143959993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001143959993 none CC[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1nc(Sc1cc(Cl)cc(Cl)c1)n2CCCNC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 8, 1, 14, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 14, 14, 14, 10, 14, 14, 14, 2, 2, 3, 5, 7, 7, 12, 12, 1, 1, 1, 1, 1, 1, 2, 14, 10, 14, 3, 3, 5, 5, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/311 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/311' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1nc(Sc1cc(Cl)cc(Cl)c1)n2CCCNC(C)C) `ZINC001143959993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001143959993 none CC[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1nc(Sc1cc(Cl)cc(Cl)c1)n2CCCNC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 8, 1, 14, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 14, 14, 14, 10, 14, 14, 14, 2, 2, 3, 5, 7, 7, 12, 12, 1, 1, 1, 1, 1, 1, 2, 14, 10, 14, 3, 3, 5, 5, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143959993 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 Building ZINC001143959993 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143959993 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 310) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1nc(Sc1cc(Cl)cc(Cl)c1)n2CCCNC(C)C) `ZINC001143959993.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143959993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001143959993 none CC[C@@]([O-])([SiH3])C(=O)Nc1ncnc2c1nc(Sc1cc(Cl)cc(Cl)c1)n2CCCNC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 8, 1, 14, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 14, 14, 14, 10, 14, 14, 14, 2, 2, 3, 5, 7, 7, 12, 12, 1, 1, 1, 1, 1, 1, 2, 14, 10, 14, 3, 3, 5, 5, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 311) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1nc(Sc1cc(Cl)cc(Cl)c1)n2CCCNC(C)C) `ZINC001143959993.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143959993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001143959993 none CC[C@]([O-])([SiH3])C(=O)Nc1ncnc2c1nc(Sc1cc(Cl)cc(Cl)c1)n2CCCNC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 1, 8, 1, 14, 1, 1, 1, 16, 1, 1, 16, 1, 8, 5, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 6, 14, 14, 14, 10, 14, 14, 14, 2, 2, 3, 5, 7, 7, 12, 12, 1, 1, 1, 1, 1, 1, 2, 14, 10, 14, 3, 3, 5, 5, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 34, 35, 32, 5, 6, 33, 7, 2, 3, 36, 4, 37] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143959993 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143959993 Building ZINC001143967986 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143967986 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/312 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 7, 12, 12, 12, 12, 21, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 12, 12, 21, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/313 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/313' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 6, 13, 13, 13, 24, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 13, 13, 24, 24, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/314 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/314' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 7, 12, 12, 12, 12, 21, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 12, 12, 21, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/315 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/315' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 6, 13, 13, 13, 24, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 13, 13, 24, 24, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143967986 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 Building ZINC001143967986 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143967986 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 312) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 7, 12, 12, 12, 12, 21, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 12, 12, 21, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 313) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 6, 13, 13, 13, 24, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 13, 13, 24, 24, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 314) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 7, 12, 12, 12, 12, 21, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 12, 12, 21, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 315) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 6, 13, 13, 13, 24, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 13, 13, 24, 24, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143967986 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 Building ZINC001143967986 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143967986 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 312) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 7, 12, 12, 12, 12, 21, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 12, 12, 21, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 313) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 6, 13, 13, 13, 24, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 13, 13, 24, 24, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 314) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 7, 12, 12, 12, 12, 21, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 12, 12, 21, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 315) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 6, 13, 13, 13, 24, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 13, 13, 24, 24, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143967986 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 Building ZINC001143967986 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001143967986 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 312) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/312: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 7, 12, 12, 12, 12, 21, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 12, 12, 21, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 313) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/313: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 6, 13, 13, 13, 24, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 13, 13, 24, 24, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 314) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/314: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 7, 12, 12, 12, 12, 21, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 3, 12, 12, 21, 21, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 315) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/315: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1) `ZINC001143967986.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001143967986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001143967986 none CC[C@]([O-])([SiH3])C(=O)Nc1c(Br)cc(Br)cc1CN(C)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 17, 1, 1, 17, 1, 1, 5, 10, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 4, 6, 13, 13, 13, 24, 32, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 4, 13, 13, 24, 24, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143967986 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143967986 Building ZINC001143968039 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143968039 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/316 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1) `ZINC001143968039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143968039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001143968039 none CC[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [0, 1, 2, 35, 4, 33, 6, 32, 7, 34, 3, 36, 5, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/317 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/317' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1) `ZINC001143968039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143968039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001143968039 none CC[C@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [0, 1, 2, 35, 4, 33, 6, 32, 7, 34, 3, 36, 5, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143968039 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 Building ZINC001143968039 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143968039 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 316) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1) `ZINC001143968039.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143968039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001143968039 none CC[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [0, 1, 2, 35, 4, 33, 6, 32, 7, 34, 3, 36, 5, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 317) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC[C@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1) `ZINC001143968039.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143968039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001143968039 none CC[C@]([O-])([SiH3])C(=O)Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 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, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 4] 50 rigid atoms, others: [0, 1, 2, 35, 4, 33, 6, 32, 7, 34, 3, 36, 5, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143968039 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143968039 Building ZINC001143971978 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971978 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/318 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)N[C@H](COc1cncc(c2ccc3n[nH]c(C)c3c2)c1)Cc1c[nH]c2ccccc12) `ZINC001143971978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001143971978 none CC[C@@]([O-])([SiH3])C(=O)N[C@H](COc1cncc(c2ccc3n[nH]c(C)c3c2)c1)Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 1, 1, 1, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 5, 5, 12, 20, 32, 32, 32, 32, 32, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 32, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 43, 43, 43, 43, 43, 43, 32, 7, 7, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 41, 42, 43, 44, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/319 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/319' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)N[C@H](COc1cncc(c2ccc3n[nH]c(C)c3c2)c1)Cc1c[nH]c2ccccc12) `ZINC001143971978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001143971978 none CC[C@]([O-])([SiH3])C(=O)N[C@H](COc1cncc(c2ccc3n[nH]c(C)c3c2)c1)Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 1, 1, 1, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 18, 27, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 5, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 2, 9, 9, 27, 27, 36, 36, 36, 36, 36, 36, 27, 8, 8, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 41, 42, 43] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143971978 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 Building ZINC001143971978 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143971978 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 318) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC[C@@]([O-])([SiH3])C(=O)N[C@H](COc1cncc(c2ccc3n[nH]c(C)c3c2)c1)Cc1c[nH]c2ccccc12) `ZINC001143971978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143971978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001143971978 none CC[C@@]([O-])([SiH3])C(=O)N[C@H](COc1cncc(c2ccc3n[nH]c(C)c3c2)c1)Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 1, 1, 1, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 5, 5, 12, 20, 32, 32, 32, 32, 32, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 32, 5, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 12, 12, 32, 32, 43, 43, 43, 43, 43, 43, 32, 7, 7, 10, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 41, 42, 43, 44, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 319) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC[C@]([O-])([SiH3])C(=O)N[C@H](COc1cncc(c2ccc3n[nH]c(C)c3c2)c1)Cc1c[nH]c2ccccc12) `ZINC001143971978.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143971978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001143971978 none CC[C@]([O-])([SiH3])C(=O)N[C@H](COc1cncc(c2ccc3n[nH]c(C)c3c2)c1)Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 5, 1, 1, 1, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 18, 27, 27, 27, 27, 27, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 27, 5, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 2, 9, 9, 27, 27, 36, 36, 36, 36, 36, 36, 27, 8, 8, 13, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 39, 40, 41, 42, 43] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 104 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143971978 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143971978 Building ZINC001143972125 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972125 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/320 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3nc4ccn5c(O)nnc5c4cc3c3ccccc3)cc2)CCC1) `ZINC001143972125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001143972125 none CC[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3nc4ccn5c(O)nnc5c4cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 7, 18, 18, 10, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 50, 50, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 4, 18, 18, 50, 50, 150, 50, 50, 50, 47, 50, 50, 18, 18, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/321 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/321' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3nc4ccn5c(O)nnc5c4cc3c3ccccc3)cc2)CCC1) `ZINC001143972125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001143972125 none CC[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3nc4ccn5c(O)nnc5c4cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 8, 19, 19, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 4, 19, 19, 50, 50, 150, 50, 50, 50, 50, 50, 50, 19, 19, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143972125 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 Building ZINC001143972125 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001143972125 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 320) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3nc4ccn5c(O)nnc5c4cc3c3ccccc3)cc2)CCC1) `ZINC001143972125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001143972125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001143972125 none CC[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3nc4ccn5c(O)nnc5c4cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 7, 18, 18, 10, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 47, 50, 50, 18, 18, 7, 7, 7, 1, 1, 1, 1, 1, 4, 18, 18, 50, 50, 150, 50, 50, 50, 47, 50, 50, 18, 18, 7, 7, 7, 7, 7, 7] 150 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 253 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 321) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3nc4ccn5c(O)nnc5c4cc3c3ccccc3)cc2)CCC1) `ZINC001143972125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001143972125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 2 is the cov attach 4 2 0 4 2 1 4 2 2 3 2 2 5 to be deleted 6 to be deleted 7 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001143972125 none CC[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3nc4ccn5c(O)nnc5c4cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['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.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.2', 'O.3', 'N.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 1, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 8, 19, 19, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 8, 8, 8, 1, 1, 1, 1, 1, 4, 19, 19, 50, 50, 150, 50, 50, 50, 50, 50, 50, 19, 19, 8, 8, 8, 8, 8, 8] 150 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 261 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001143972125 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001143972125 Building ZINC001144039883 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144039883 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/322 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(c2cn(CCc3ccsc3)nn2)cc1) `ZINC001144039883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144039883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001144039883 none CCC[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(c2cn(CCc3ccsc3)nn2)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 14, 1, 8, 8, 1, 1, 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] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 4, 6, 17, 17, 17, 27, 27, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 6, 6, 17, 27, 27, 27, 27, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 3, 4, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/323 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/323' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(c2cn(CCc3ccsc3)nn2)cc1) `ZINC001144039883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144039883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001144039883 none CCC[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(c2cn(CCc3ccsc3)nn2)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 14, 1, 8, 8, 1, 1, 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] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 4, 4, 18, 18, 18, 28, 28, 50, 50, 50, 50, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 6, 6, 18, 28, 28, 28, 28, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 3, 4, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001144039883 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 Building ZINC001144039883 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001144039883 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 322) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCC[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(c2cn(CCc3ccsc3)nn2)cc1) `ZINC001144039883.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001144039883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001144039883 none CCC[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(c2cn(CCc3ccsc3)nn2)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 14, 1, 8, 8, 1, 1, 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] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 4, 6, 17, 17, 17, 27, 27, 50, 50, 50, 50, 17, 17, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 6, 6, 17, 27, 27, 27, 27, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 3, 4, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 323) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCC[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(c2cn(CCc3ccsc3)nn2)cc1) `ZINC001144039883.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001144039883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 3 is the cov attach 4 3 0 4 3 1 4 3 2 3 3 2 6 to be deleted 7 to be deleted 8 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001144039883 none CCC[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(c2cn(CCc3ccsc3)nn2)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', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 1, 14, 1, 8, 8, 1, 1, 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] dock color type numbers: [7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 4, 4, 18, 18, 18, 28, 28, 50, 50, 50, 50, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 6, 6, 18, 28, 28, 28, 28, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 3, 4, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001144039883 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001144039883 Building ZINC001180962394 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180962394 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/324 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)cc1OC) `ZINC001180962394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180962394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180962394 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 10, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 30, 30, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/325 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/325' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)cc1OC) `ZINC001180962394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180962394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180962394 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 9, 8, 9, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 30, 30, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180962394 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 Building ZINC001180962394 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180962394 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 324) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)cc1OC) `ZINC001180962394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180962394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180962394 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 10, 8, 10, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 30, 30, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 53, 54, 55, 56]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 325) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)cc1OC) `ZINC001180962394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180962394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001180962394 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 30, 30, 30, 30, 9, 8, 9, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 50, 50, 50, 50, 30, 30, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 50, 50, 50] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 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/281161/xco-8058088.67/working/building/ZINC001180962394 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180962394 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180962394 Building ZINC001180964164 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964164 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/326 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Br)c(C(F)(F)F)c1Br)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180964164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001180964164 none O=C(Nc1ncc(Br)c(C(F)(F)F)c1Br)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 17, 1, 5, 15, 15, 15, 1, 17, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 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] 0 hydrogens need 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, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 7, 7, 13, 13, 7, 13, 13, 5, 29, 7, 7, 7, 7, 13, 13, 7, 13, 13] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/327 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/327' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Br)c(C(F)(F)F)c1Br)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180964164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001180964164 none O=C(Nc1ncc(Br)c(C(F)(F)F)c1Br)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 17, 1, 5, 15, 15, 15, 1, 17, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 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] 0 hydrogens need 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 12, 12, 8, 12, 12, 5, 28, 7, 7, 7, 7, 12, 12, 12, 12, 12] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180964164 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 Building ZINC001180964164 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964164 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 326) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/326: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Br)c(C(F)(F)F)c1Br)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180964164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001180964164 none O=C(Nc1ncc(Br)c(C(F)(F)F)c1Br)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 17, 1, 5, 15, 15, 15, 1, 17, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 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] 0 hydrogens need 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, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 7, 7, 13, 13, 7, 13, 13, 5, 29, 7, 7, 7, 7, 13, 13, 7, 13, 13] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 327) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/327: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Br)c(C(F)(F)F)c1Br)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180964164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001180964164 none O=C(Nc1ncc(Br)c(C(F)(F)F)c1Br)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'Br', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 17, 1, 5, 15, 15, 15, 1, 17, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 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] 0 hydrogens need 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, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 7, 7, 12, 12, 8, 12, 12, 5, 28, 7, 7, 7, 7, 12, 12, 12, 12, 12] 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: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180964164 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964164 Building ZINC001180964185 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964185 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/328 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)c(Br)n2)c1) `ZINC001180964185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001180964185 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 50, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 26, 50, 50, 50, 50, 50, 26, 26, 26, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/329 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/329' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])CCc3ccccc3)c(Br)n2)c1) `ZINC001180964185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001180964185 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])CCc3ccccc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 50, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 25, 50, 50, 50, 50, 50, 25, 25, 25, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180964185 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 Building ZINC001180964185 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964185 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 328) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOC(=O)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)c(Br)n2)c1) `ZINC001180964185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001180964185 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 26, 50, 26, 26, 26, 26, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 26, 50, 50, 50, 50, 50, 26, 26, 26, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 329) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOC(=O)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])CCc3ccccc3)c(Br)n2)c1) `ZINC001180964185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001180964185 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])CCc3ccccc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 25, 50, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 25, 50, 50, 50, 50, 50, 25, 25, 25, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180964185 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964185 Building ZINC001180964942 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964942 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/330 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC[C@@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180964942.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180964942 none CC(C)(C)OC(=O)N1CCC2(CC[C@@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 9, 14, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 5, 5, 12, 12, 5, 12, 12, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 12, 12, 5, 12, 12, 9, 9, 9, 9] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 331) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180964942.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180964942 none CC(C)(C)OC(=O)N1CCC2(CC[C@@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 9, 14, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 5, 5, 12, 12, 5, 12, 12, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 12, 12, 5, 12, 12, 9, 9, 9, 9] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180964942 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 Building ZINC001180964942 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964942 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 330) grep: /scratch/xiaobo/281161/xco-8058088.67/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 Failed to generate 3D embedding in both batch and single-runs Skipping ZINC001180964942 0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 `0' -> `0.failed' Finished preparing ZINC001180964942 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Found failed protomers Marking ZINC001180964942 as failed mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/failed' `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964942' -> `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942' Building ZINC001180964943 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964943 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/332 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180964943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180964943 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 8, 8, 4, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 82 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 333) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180964943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180964943 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 8, 8, 4, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 82 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180964943 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 Building ZINC001180964943 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180964943 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 332) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180964943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180964943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180964943 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 5, 5, 8, 8, 5, 8, 8, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 8, 8, 5, 8, 8, 9, 9, 9, 9] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 333) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180964943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180964943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001180964943 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])CCc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 3, 10, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 3, 3, 25, 25, 25, 25, 25, 25, 25, 25, 25, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 8, 8, 4, 8, 8, 3, 3, 3, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 82 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180964943 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180964943 Building ZINC001180965060 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965060 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/334 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001180965060 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 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] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 7, 43, 46, 46, 43, 46, 46, 13, 13, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 7, 13, 13, 46, 46, 43, 46, 46, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 335) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001180965060 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 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] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 7, 43, 46, 46, 43, 46, 46, 13, 13, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 7, 13, 13, 46, 46, 43, 46, 46, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965060 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 Building ZINC001180965060 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965060 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 334) grep: /scratch/xiaobo/281161/xco-8058088.67/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(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001180965060 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 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] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 11, 14, 43, 46, 46, 43, 46, 46, 14, 14, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 7, 14, 14, 46, 46, 43, 46, 46, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 335) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001180965060 none O=C(Nc1ncnc2[nH]nc(c3ccc(Oc4ccccc4)cc3)c21)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 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] dock color type numbers: [6, 9, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 7, 7, 43, 46, 46, 43, 46, 46, 13, 13, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 7, 13, 13, 46, 46, 43, 46, 46, 13, 13, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965060 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965060 Building ZINC001180965144 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965144 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/336 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc(S(=O)(=O)N2CCCc3ccccc32)ccc1Cl)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001180965144 none O=C(Nc1cc(S(=O)(=O)N2CCCc3ccccc32)ccc1Cl)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 35, 35, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 8, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 337) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(S(=O)(=O)N2CCCc3ccccc32)ccc1Cl)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001180965144 none O=C(Nc1cc(S(=O)(=O)N2CCCc3ccccc32)ccc1Cl)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 35, 35, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 8, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965144 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 Building ZINC001180965144 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965144 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 336) grep: /scratch/xiaobo/281161/xco-8058088.67/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(Nc1cc(S(=O)(=O)N2CCCc3ccccc32)ccc1Cl)[C@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965144.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001180965144 none O=C(Nc1cc(S(=O)(=O)N2CCCc3ccccc32)ccc1Cl)[C@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 35, 35, 42, 48, 48, 48, 48, 48, 48, 48, 48, 48, 8, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 8, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 337) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(S(=O)(=O)N2CCCc3ccccc32)ccc1Cl)[C@@]([O-])([SiH3])CCc1ccccc1) `ZINC001180965144.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 59 natoms 58 natoms 57 natoms 56 names: ZINC001180965144 none O=C(Nc1cc(S(=O)(=O)N2CCCc3ccccc32)ccc1Cl)[C@@]([O-])([SiH3])CCc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 14, 11, 11, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 35, 35, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 8, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 3, 8, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965144 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965144 Building ZINC001180965348 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965348 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/338 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180965348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001180965348 none CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations 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, 35, 49, 35, 35, 35, 24, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [27, 54, 60, 57, 55, 59, 56, 58, 20, 53, 22, 23, 24, 25, 26, 31, 28, 29, 30, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 339) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Oc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180965348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001180965348 none CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations 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, 35, 49, 35, 35, 35, 24, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [27, 54, 60, 57, 55, 59, 56, 58, 20, 53, 22, 23, 24, 25, 26, 31, 28, 29, 30, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965348 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 Building ZINC001180965348 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965348 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 338) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180965348.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001180965348 none CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations 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, 34, 49, 34, 34, 34, 25, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 34, 34, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [27, 54, 60, 57, 55, 59, 56, 58, 20, 53, 22, 23, 24, 25, 26, 31, 28, 29, 30, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 339) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Oc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)CC1) `ZINC001180965348.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001180965348 none CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)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', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 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] 0 hydrogens need rotated 50 conformations 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, 35, 49, 35, 35, 35, 24, 4, 4, 4, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [27, 54, 60, 57, 55, 59, 56, 58, 20, 53, 22, 23, 24, 25, 26, 31, 28, 29, 30, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 61, 62, 63, 64]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965348 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965348 Building ZINC001180965362 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965362 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/340 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2ncnc(N(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)c3cccc(Br)c3)c2c1) `ZINC001180965362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001180965362 none Nc1ccc2ncnc(N(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)c3cccc(Br)c3)c2c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 13, 6, 1, 6, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 13, 34, 34, 26, 34, 34, 34, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 6, 6, 6, 6, 6, 34, 34, 34, 34, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 341) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2ncnc(N(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)c3cccc(Br)c3)c2c1) `ZINC001180965362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001180965362 none Nc1ccc2ncnc(N(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)c3cccc(Br)c3)c2c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 13, 6, 1, 6, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 13, 34, 34, 26, 34, 34, 34, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 6, 6, 6, 6, 6, 34, 34, 34, 34, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965362 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 Building ZINC001180965362 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965362 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 340) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Nc1ccc2ncnc(N(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)c3cccc(Br)c3)c2c1) `ZINC001180965362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001180965362 none Nc1ccc2ncnc(N(C(=O)[C@]([O-])([SiH3])CCc3ccccc3)c3cccc(Br)c3)c2c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 13, 6, 1, 6, 1, 1, 1, 5, 5, 6, 6, 5, 6, 6, 13, 31, 31, 31, 31, 31, 31, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 6, 6, 5, 6, 6, 31, 31, 31, 31, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 341) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccc2ncnc(N(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)c3cccc(Br)c3)c2c1) `ZINC001180965362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001180965362 none Nc1ccc2ncnc(N(C(=O)[C@@]([O-])([SiH3])CCc3ccccc3)c3cccc(Br)c3)c2c1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 3, 7, 3, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 13, 6, 1, 6, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 13, 34, 34, 26, 34, 34, 34, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 5, 6, 6, 6, 6, 6, 34, 34, 34, 34, 18] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965362 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965362 Building ZINC001180965478 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965478 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/342 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)cc1N) `ZINC001180965478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001180965478 none CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 22, 26, 10, 10, 10, 10, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 26, 26, 26, 26, 26, 22, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 343) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])CCc2ccccc2)cc1N) `ZINC001180965478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001180965478 none CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])CCc2ccccc2)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 22, 26, 10, 10, 10, 10, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 26, 26, 26, 26, 26, 22, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965478 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 Building ZINC001180965478 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965478 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 342) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)cc1N) `ZINC001180965478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001180965478 none CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])CCc2ccccc2)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 9, 9, 9, 9, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 24, 24, 24, 24, 24, 21, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 343) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])CCc2ccccc2)cc1N) `ZINC001180965478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001180965478 none CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])CCc2ccccc2)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 22, 26, 10, 10, 10, 10, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 26, 26, 26, 26, 26, 22, 10, 10, 10, 10, 10, 10, 10, 10, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965478 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965478 Building ZINC001180965743 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965743 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/344 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c([nH]1)-c1ccccc1N(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)cc1)CC2) `ZINC001180965743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001180965743 none Cc1nc2c([nH]1)-c1ccccc1N(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 45, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [32, 53, 55, 47, 48, 49, 50, 51, 52, 21, 54, 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, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 345) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c([nH]1)-c1ccccc1N(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])CCc3ccccc3)cc1)CC2) `ZINC001180965743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001180965743 none Cc1nc2c([nH]1)-c1ccccc1N(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])CCc3ccccc3)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 45, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [32, 53, 55, 47, 48, 49, 50, 51, 52, 21, 54, 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, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965743 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 Building ZINC001180965743 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180965743 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 344) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1nc2c([nH]1)-c1ccccc1N(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)cc1)CC2) `ZINC001180965743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180965743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001180965743 none Cc1nc2c([nH]1)-c1ccccc1N(C(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])CCc3ccccc3)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 45, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [32, 53, 55, 47, 48, 49, 50, 51, 52, 21, 54, 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, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58, 59, 60, 61]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 345) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2c([nH]1)-c1ccccc1N(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])CCc3ccccc3)cc1)CC2) `ZINC001180965743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180965743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001180965743 none Cc1nc2c([nH]1)-c1ccccc1N(C(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])CCc3ccccc3)cc1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 18, 45, 8, 14, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [32, 53, 55, 47, 48, 49, 50, 51, 52, 21, 54, 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, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 56, 57, 58, 59, 60, 61]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180965743 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180965743 Building ZINC001180969880 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180969880 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/346 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21) `ZINC001180969880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180969880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180969880 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 25, 36, 25, 25, 25, 9, 25, 3, 1, 3, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 25, 25, 25, 25, 25, 25, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 25, 25, 25, 25, 3, 4, 4, 4, 4, 6, 6, 4, 6, 6, 25, 25, 25] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 347) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21) `ZINC001180969880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180969880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180969880 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 25, 36, 25, 25, 25, 9, 25, 3, 1, 3, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 25, 25, 25, 25, 25, 25, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 25, 25, 25, 25, 3, 4, 4, 4, 4, 6, 6, 4, 6, 6, 25, 25, 25] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180969880 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 Building ZINC001180969880 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180969880 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 346) grep: /scratch/xiaobo/281161/xco-8058088.67/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)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21) `ZINC001180969880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180969880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180969880 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 20, 27, 20, 20, 20, 9, 20, 3, 1, 3, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 20, 20, 20, 20, 20, 20, 20, 42, 42, 42, 42, 42, 42, 42, 42, 42, 20, 20, 20, 20, 3, 4, 4, 4, 4, 6, 6, 4, 6, 6, 20, 20, 20] 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]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 347) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21) `ZINC001180969880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180969880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180969880 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 25, 36, 25, 25, 25, 9, 25, 3, 1, 3, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 25, 25, 25, 25, 25, 25, 25, 44, 44, 44, 44, 44, 44, 44, 44, 44, 25, 25, 25, 25, 3, 4, 4, 4, 4, 6, 6, 4, 6, 6, 25, 25, 25] 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180969880 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969880 Building ZINC001180969881 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180969881 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/348 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21) `ZINC001180969881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180969881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180969881 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 19, 24, 19, 19, 19, 12, 19, 3, 1, 3, 1, 1, 1, 4, 4, 5, 5, 4, 5, 5, 19, 19, 19, 19, 19, 19, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 19, 19, 19, 3, 4, 4, 4, 4, 5, 5, 4, 5, 5, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 349) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21) `ZINC001180969881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180969881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180969881 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 19, 24, 19, 19, 19, 12, 19, 3, 1, 3, 1, 1, 1, 4, 4, 5, 5, 4, 5, 5, 19, 19, 19, 19, 19, 19, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 19, 19, 19, 3, 4, 4, 4, 4, 5, 5, 4, 5, 5, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180969881 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 Building ZINC001180969881 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001180969881 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 348) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21) `ZINC001180969881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001180969881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180969881 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 23, 29, 23, 23, 23, 10, 23, 3, 1, 3, 1, 1, 1, 4, 4, 5, 5, 4, 5, 5, 23, 23, 23, 23, 23, 23, 23, 44, 44, 44, 44, 44, 44, 44, 44, 44, 23, 23, 23, 23, 3, 4, 4, 4, 4, 5, 5, 4, 5, 5, 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, 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/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 349) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21) `ZINC001180969881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001180969881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001180969881 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])CCc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 19, 24, 19, 19, 19, 12, 19, 3, 1, 3, 1, 1, 1, 4, 4, 5, 5, 4, 5, 5, 19, 19, 19, 19, 19, 19, 19, 39, 39, 39, 39, 39, 39, 39, 39, 39, 19, 19, 19, 19, 3, 4, 4, 4, 4, 5, 5, 4, 5, 5, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001180969881 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001180969881 Building ZINC001181374403 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181374403 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/350 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc1) `ZINC001181374403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181374403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001181374403 none COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 32, 45, 45, 32, 13, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45, 45, 32, 32, 13, 7, 7, 7, 7, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 45, 45] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 210 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 351) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc1) `ZINC001181374403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181374403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001181374403 none COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 32, 45, 45, 32, 13, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45, 45, 32, 32, 13, 7, 7, 7, 7, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 45, 45] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 210 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181374403 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 Building ZINC001181374403 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181374403 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 350) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc1) `ZINC001181374403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181374403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001181374403 none COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 34, 45, 45, 34, 13, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45, 45, 34, 34, 13, 7, 7, 7, 7, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 45, 45] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 206 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 351) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc1) `ZINC001181374403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181374403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001181374403 none COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 43, 32, 45, 45, 32, 13, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 45, 45, 45, 45, 45, 45, 45, 32, 32, 13, 7, 7, 7, 7, 7, 7, 7, 3, 5, 5, 5, 5, 5, 5, 5, 45, 45] 50 rigid atoms, others: [24, 25, 26, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 210 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181374403 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374403 Building ZINC001181374943 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181374943 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/352 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CC2)c2cc(Cl)ccc21) `ZINC001181374943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181374943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001181374943 none CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CC2)c2cc(Cl)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 20, 12, 12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 353) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CC2)c2cc(Cl)ccc21) `ZINC001181374943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181374943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001181374943 none CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CC2)c2cc(Cl)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 20, 12, 12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181374943 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 Building ZINC001181374943 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181374943 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 352) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/352: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CC2)c2cc(Cl)ccc21) `ZINC001181374943.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181374943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001181374943 none CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CC2)c2cc(Cl)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 13, 21, 13, 13, 13, 13, 13, 8, 2, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 37, 37, 37, 37, 37, 37, 37, 37, 37, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 353) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CC2)c2cc(Cl)ccc21) `ZINC001181374943.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181374943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001181374943 none CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CC2)c2cc(Cl)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 12, 20, 12, 12, 12, 12, 12, 8, 2, 9, 1, 1, 1, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 36, 36, 36, 36, 36, 36, 36, 36, 36, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 7, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [16, 17, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181374943 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181374943 Building ZINC001181375235 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181375235 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/354 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc(OC)c1OC) `ZINC001181375235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181375235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001181375235 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 9, 9, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 13, 3, 5, 15, 13, 13, 13, 9, 3, 12, 12, 12, 24, 12, 3, 2, 2, 2, 2, 2, 2, 2, 2, 9, 13, 13, 13, 15, 15, 15] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 355) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc(OC)c1OC) `ZINC001181375235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181375235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001181375235 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 9, 9, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 13, 3, 5, 15, 13, 13, 13, 9, 3, 12, 12, 12, 24, 12, 3, 2, 2, 2, 2, 2, 2, 2, 2, 9, 13, 13, 13, 15, 15, 15] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181375235 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 Building ZINC001181375235 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181375235 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 354) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc(OC)c1OC) `ZINC001181375235.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181375235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001181375235 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 10, 10, 10, 4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 13, 4, 4, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 10, 10, 10, 14, 6, 6, 15, 13, 13, 13, 10, 4, 13, 13, 13, 26, 13, 4, 2, 2, 2, 2, 2, 2, 2, 2, 10, 14, 14, 14, 15, 15, 15] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 355) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc(OC)c1OC) `ZINC001181375235.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181375235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001181375235 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 9, 9, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 9, 9, 13, 3, 5, 15, 13, 13, 13, 9, 3, 12, 12, 12, 24, 12, 3, 2, 2, 2, 2, 2, 2, 2, 2, 9, 13, 13, 13, 15, 15, 15] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181375235 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181375235 Building ZINC001181376130 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376130 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/356 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C3CCN(C(=O)[C@@]([O-])([SiH3])Cc4ccccc4)CC3)oc2c(Br)c1) `ZINC001181376130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001181376130 none COc1cc2cc(C3CCN(C(=O)[C@@]([O-])([SiH3])Cc4ccccc4)CC3)oc2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 43, 43, 43, 38, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 357) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C3CCN(C(=O)[C@]([O-])([SiH3])Cc4ccccc4)CC3)oc2c(Br)c1) `ZINC001181376130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001181376130 none COc1cc2cc(C3CCN(C(=O)[C@]([O-])([SiH3])Cc4ccccc4)CC3)oc2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 43, 43, 43, 38, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376130 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 Building ZINC001181376130 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376130 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 356) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1cc2cc(C3CCN(C(=O)[C@@]([O-])([SiH3])Cc4ccccc4)CC3)oc2c(Br)c1) `ZINC001181376130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001181376130 none COc1cc2cc(C3CCN(C(=O)[C@@]([O-])([SiH3])Cc4ccccc4)CC3)oc2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 34, 34, 34, 34, 34, 7, 7, 7, 7, 4, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 34, 34, 34, 34, 34, 38, 38, 38, 34, 34, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 34] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 357) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc2cc(C3CCN(C(=O)[C@]([O-])([SiH3])Cc4ccccc4)CC3)oc2c(Br)c1) `ZINC001181376130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001181376130 none COc1cc2cc(C3CCN(C(=O)[C@]([O-])([SiH3])Cc4ccccc4)CC3)oc2c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 38, 38, 38, 38, 6, 6, 6, 6, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 38, 38, 38, 38, 38, 43, 43, 43, 38, 38, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376130 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376130 Building ZINC001181376236 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376236 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/358 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(F)cc(CN(C(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001181376236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001181376236 none Cc1cc(F)cc(CN(C(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 10, 10, 15, 15, 15, 15, 15, 15, 8, 8, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 99 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 359) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(F)cc(CN(C(=O)[C@]([O-])([SiH3])Cc2ccccc2)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001181376236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001181376236 none Cc1cc(F)cc(CN(C(=O)[C@]([O-])([SiH3])Cc2ccccc2)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 10, 10, 15, 15, 15, 15, 15, 15, 8, 8, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 99 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376236 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 Building ZINC001181376236 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376236 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 358) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(F)cc(CN(C(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001181376236.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001181376236 none Cc1cc(F)cc(CN(C(=O)[C@@]([O-])([SiH3])Cc2ccccc2)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 8, 6, 4, 1, 4, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 9, 9, 17, 17, 17, 17, 17, 17, 8, 8, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 16, 16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 9, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 102 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 359) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(F)cc(CN(C(=O)[C@]([O-])([SiH3])Cc2ccccc2)C2CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001181376236.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001181376236 none Cc1cc(F)cc(CN(C(=O)[C@]([O-])([SiH3])Cc2ccccc2)C2CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 10, 10, 15, 15, 15, 15, 15, 15, 8, 8, 4, 4, 4, 4, 4, 4, 4, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 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, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 99 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376236 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376236 Building ZINC001181376519 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376519 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/360 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001181376519 none COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 9, 9, 9, 9, 9, 9, 5, 3, 5, 10, 10, 16, 16, 16, 32, 16, 16, 16, 16, 16, 25, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 15, 15, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 16, 32, 32, 32, 16, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 151 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 361) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001181376519 none COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 9, 9, 9, 9, 9, 9, 5, 3, 5, 10, 10, 16, 16, 16, 32, 16, 16, 16, 16, 16, 25, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 15, 15, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 16, 32, 32, 32, 16, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 151 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376519 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 Building ZINC001181376519 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376519 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 360) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001181376519 none COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 5, 3, 5, 10, 10, 15, 15, 15, 30, 15, 15, 15, 15, 15, 26, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 11, 11, 11, 8, 8, 8, 8, 8, 8, 10, 10, 10, 10, 15, 30, 30, 30, 15, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 140 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 361) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181376519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001181376519 none COc1ccccc1CN(CCc1cc(OC)c(Cl)cc1OC)C(=O)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 8, 5, 5, 1, 1, 1, 12, 5, 1, 16, 1, 1, 12, 5, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 9, 9, 9, 9, 9, 9, 5, 3, 5, 10, 10, 16, 16, 16, 32, 16, 16, 16, 16, 16, 25, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 15, 15, 15, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 16, 32, 32, 32, 16, 25, 25, 25, 7, 7, 7, 7, 7, 7, 7] 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]) total number of confs: 151 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376519 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376519 Building ZINC001181376673 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376673 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/362 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])Cc2ccccc2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001181376673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001181376673 none Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])Cc2ccccc2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 5, 5, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 13, 22, 22, 37, 38, 38, 38, 3, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 138 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 363) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])Cc2ccccc2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001181376673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001181376673 none Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])Cc2ccccc2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 5, 5, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 13, 22, 22, 37, 38, 38, 38, 3, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 138 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376673 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 Building ZINC001181376673 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376673 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 362) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])Cc2ccccc2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001181376673.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001181376673 none Cc1ccc(CN(C(=O)[C@]([O-])([SiH3])Cc2ccccc2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 4, 4, 3, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 13, 23, 23, 39, 39, 39, 39, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 13, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 3, 3, 3, 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, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 123 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 363) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])Cc2ccccc2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1) `ZINC001181376673.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 73 natoms 72 natoms 71 natoms 70 names: ZINC001181376673 none Cc1ccc(CN(C(=O)[C@@]([O-])([SiH3])Cc2ccccc2)[C@H]2CC[C@H](NC(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 5, 5, 3, 3, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 13, 22, 22, 37, 38, 38, 38, 3, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 13, 38, 38, 38, 38, 38, 38, 38, 38, 38, 3, 3, 3, 3, 5, 5] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 138 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376673 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376673 Building ZINC001181376713 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376713 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/364 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1) `ZINC001181376713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001181376713 none COc1ccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 11, 11, 26, 26, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 25, 11, 11, 28, 11, 11, 26, 26, 26, 26, 26, 26, 26, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 25, 25, 25, 28, 28, 28, 11, 26, 26] 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]) total number of confs: 174 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 365) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]2CN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1) `ZINC001181376713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001181376713 none COc1ccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 11, 11, 26, 26, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 25, 11, 11, 28, 11, 11, 26, 26, 26, 26, 26, 26, 26, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 25, 25, 25, 28, 28, 28, 11, 26, 26] 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]) total number of confs: 174 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376713 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 Building ZINC001181376713 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376713 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 364) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1) `ZINC001181376713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001181376713 none COc1ccc([C@H]2CN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 10, 21, 21, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 21, 10, 10, 26, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10, 10, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 21, 21, 21, 26, 26, 26, 10, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 143 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 365) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]2CN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1) `ZINC001181376713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001181376713 none COc1ccc([C@H]2CN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 11, 11, 26, 26, 11, 11, 11, 11, 10, 1, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 11, 11, 11, 25, 11, 11, 28, 11, 11, 26, 26, 26, 26, 26, 26, 26, 11, 11, 7, 7, 7, 7, 7, 7, 7, 11, 11, 11, 11, 25, 25, 25, 28, 28, 28, 11, 26, 26] 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]) total number of confs: 174 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376713 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376713 Building ZINC001181376717 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376717 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/366 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1) `ZINC001181376717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001181376717 none COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 10, 21, 21, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 20, 10, 10, 25, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10, 10, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 20, 20, 20, 25, 25, 25, 10, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 367) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]2CN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1) `ZINC001181376717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001181376717 none COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 10, 21, 21, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 20, 10, 10, 25, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10, 10, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 20, 20, 20, 25, 25, 25, 10, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376717 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 Building ZINC001181376717 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181376717 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 366) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1) `ZINC001181376717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181376717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001181376717 none COc1ccc([C@@H]2CN(C(=O)[C@@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 9, 9, 24, 24, 9, 9, 9, 9, 8, 1, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 20, 9, 9, 22, 9, 9, 24, 24, 24, 24, 24, 24, 24, 9, 9, 8, 8, 8, 8, 8, 8, 8, 9, 9, 9, 9, 20, 20, 20, 22, 22, 22, 9, 24, 24] 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]) total number of confs: 164 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 367) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]2CN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1) `ZINC001181376717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181376717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001181376717 none COc1ccc([C@@H]2CN(C(=O)[C@]([O-])([SiH3])Cc3ccccc3)CCc3c(Cl)c(OC)c(OC)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.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.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 16, 1, 12, 5, 1, 12, 5, 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] dock color type numbers: [7, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 10, 10, 21, 21, 10, 10, 10, 10, 8, 1, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 10, 10, 20, 10, 10, 25, 10, 10, 21, 21, 21, 21, 21, 21, 21, 10, 10, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 20, 20, 20, 25, 25, 25, 10, 21, 21] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 142 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181376717 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181376717 Building ZINC001181379449 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001181379449 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/368 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/369 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/369' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 15, 26, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/370 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/370' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 371) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181379449 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 Building ZINC001181379449 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001181379449 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 368) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 15, 26, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 369) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 370) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 15, 26, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 371) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181379449 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 Building ZINC001181379449 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001181379449 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 368) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 15, 26, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 369) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 370) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 15, 26, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 371) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181379449 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 Building ZINC001181379449 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001181379449 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 368) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/368: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 15, 26, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 369) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/369: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 370) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/370: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 15, 26, 37, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 371) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1) `ZINC001181379449.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001181379449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 30 is the cov attach 4 30 0 4 30 1 4 30 2 3 30 2 33 to be deleted 34 to be deleted 35 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001181379449 none O=C(NCCCCN(Cc1nc2ccccc2[nH]1)[C@H]1CCCc2cccnc21)[C@@]([O-])([SiH3])Cc1ccccc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 6, 5, 7, 5, 5, 5, 1, 1, 1, 1, 8, 1, 5, 12, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 3, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 14, 26, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 17, 17, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 33, 38, 39, 64, 67, 34, 35, 66, 69, 68, 36, 63, 65, 37, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 247 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181379449 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181379449 Building ZINC001181381932 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181381932 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/372 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cnc(c2ccc(C3(NC(=O)[C@]([O-])([SiH3])Cc4ccccc4)CCC3)cc2)c(c2ccccc2)c1) `ZINC001181381932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181381932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001181381932 none NC(=O)c1cnc(c2ccc(C3(NC(=O)[C@]([O-])([SiH3])Cc4ccccc4)CCC3)cc2)c(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 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: [4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 5, 8, 13, 13, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 5, 13, 13, 28, 28, 29, 29, 29, 29, 29, 28, 49, 49, 28, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 29, 29, 29, 29, 29, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 373) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cnc(c2ccc(C3(NC(=O)[C@@]([O-])([SiH3])Cc4ccccc4)CCC3)cc2)c(c2ccccc2)c1) `ZINC001181381932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181381932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001181381932 none NC(=O)c1cnc(c2ccc(C3(NC(=O)[C@@]([O-])([SiH3])Cc4ccccc4)CCC3)cc2)c(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 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: [4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 5, 8, 13, 13, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 5, 13, 13, 28, 28, 29, 29, 29, 29, 29, 28, 49, 49, 28, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 29, 29, 29, 29, 29, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181381932 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 Building ZINC001181381932 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181381932 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 372) grep: /scratch/xiaobo/281161/xco-8058088.67/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: NC(=O)c1cnc(c2ccc(C3(NC(=O)[C@]([O-])([SiH3])Cc4ccccc4)CCC3)cc2)c(c2ccccc2)c1) `ZINC001181381932.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181381932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001181381932 none NC(=O)c1cnc(c2ccc(C3(NC(=O)[C@]([O-])([SiH3])Cc4ccccc4)CCC3)cc2)c(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 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: [4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 47, 27, 27, 21, 3, 3, 14, 14, 3, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 21, 27, 27, 27, 27, 27, 27, 27, 47, 47, 27, 14, 14, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 27, 27, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 373) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cnc(c2ccc(C3(NC(=O)[C@@]([O-])([SiH3])Cc4ccccc4)CCC3)cc2)c(c2ccccc2)c1) `ZINC001181381932.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181381932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001181381932 none NC(=O)c1cnc(c2ccc(C3(NC(=O)[C@@]([O-])([SiH3])Cc4ccccc4)CCC3)cc2)c(c2ccccc2)c1 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 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: [4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 28, 49, 28, 28, 28, 5, 8, 13, 13, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 5, 5, 5, 13, 13, 28, 28, 29, 29, 29, 29, 29, 28, 49, 49, 28, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 13, 13, 29, 29, 29, 29, 29, 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, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181381932 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181381932 Building ZINC001181382087 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181382087 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/374 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21) `ZINC001181382087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181382087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181382087 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 32, 18, 32, 18, 18, 18, 9, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 375) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21) `ZINC001181382087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181382087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181382087 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 32, 18, 32, 18, 18, 18, 9, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181382087 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 Building ZINC001181382087 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181382087 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 374) grep: /scratch/xiaobo/281161/xco-8058088.67/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)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21) `ZINC001181382087.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181382087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181382087 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 23, 35, 23, 23, 23, 10, 23, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 23, 23, 23, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 3, 3, 3, 3, 3, 3, 3, 3, 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, 54]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 375) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21) `ZINC001181382087.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181382087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181382087 none CC(C)(C)OC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 32, 18, 32, 18, 18, 18, 9, 18, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 18, 3, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181382087 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382087 Building ZINC001181382095 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181382095 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/376 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21) `ZINC001181382095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181382095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181382095 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 19, 35, 19, 19, 19, 7, 19, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 377) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21) `ZINC001181382095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181382095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181382095 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 19, 35, 19, 19, 19, 7, 19, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181382095 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 Building ZINC001181382095 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001181382095 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 376) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21) `ZINC001181382095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001181382095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181382095 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 19, 35, 19, 19, 19, 9, 19, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 377) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21) `ZINC001181382095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001181382095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001181382095 none CC(C)(C)OC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])Cc2ccccc2)c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 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, 3, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 19, 35, 19, 19, 19, 7, 19, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 19, 19, 19, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 3, 3, 3, 3, 3, 3, 3, 3, 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001181382095 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001181382095 Building ZINC001182668362 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182668362 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/378 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 17, 17, 17, 5, 8, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 32, 47, 47, 47, 47, 47, 28, 28, 28, 24, 24, 17, 17, 5, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/379 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/379' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/380 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/380' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 381) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182668362 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 Building ZINC001182668362 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182668362 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 378) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 17, 17, 17, 5, 8, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 32, 47, 47, 47, 47, 47, 28, 28, 28, 24, 24, 17, 17, 5, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 379) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 17, 17, 17, 5, 8, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 32, 47, 47, 47, 47, 47, 28, 28, 28, 24, 24, 17, 17, 5, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 380) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 381) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182668362 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 Building ZINC001182668362 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182668362 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 378) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 17, 17, 17, 5, 8, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 32, 47, 47, 47, 47, 47, 28, 28, 28, 24, 24, 17, 17, 5, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 379) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 17, 17, 17, 5, 8, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 32, 47, 47, 47, 47, 47, 28, 28, 28, 24, 24, 17, 17, 5, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 380) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 381) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182668362 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 Building ZINC001182668362 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182668362 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 378) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 17, 17, 17, 5, 8, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 32, 47, 47, 47, 47, 47, 28, 28, 28, 24, 24, 17, 17, 5, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 379) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 17, 17, 17, 5, 8, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 4, 4, 32, 47, 47, 47, 47, 47, 28, 28, 28, 24, 24, 17, 17, 5, 4, 4, 4, 4, 4, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47] 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: 168 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 380) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/380: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 381) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1) `ZINC001182668362.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182668362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001182668362 none CN(Cc1cc(Br)cc(Br)c1NC(=O)[C@]([O-])([SiH3])C1CC1)C1CCCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', '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'] dock atom type numbers: [5, 10, 5, 1, 1, 1, 17, 1, 1, 17, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens 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, 24, 16, 16, 16, 4, 7, 16, 16, 16, 4, 4, 1, 4, 1, 1, 1, 5, 5, 35, 49, 49, 49, 49, 49, 31, 31, 31, 24, 24, 16, 16, 4, 5, 5, 5, 5, 5, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49] 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: 182 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182668362 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668362 Building ZINC001182668534 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182668534 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/382 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/382' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1)[C@@]([O-])([SiH3])C1CC1) `ZINC001182668534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182668534 none O=C(Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 5, 12, 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, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 51, 52, 53, 54, 55, 27, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 383) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1)[C@]([O-])([SiH3])C1CC1) `ZINC001182668534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182668534 none O=C(Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 5, 12, 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, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 51, 52, 53, 54, 55, 27, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182668534 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 Building ZINC001182668534 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182668534 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 382) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/382: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1)[C@@]([O-])([SiH3])C1CC1) `ZINC001182668534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182668534 none O=C(Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1)[C@@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 5, 12, 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, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 4, 4, 18, 18, 18, 18, 18, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 51, 52, 53, 54, 55, 27, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 383) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1)[C@]([O-])([SiH3])C1CC1) `ZINC001182668534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182668534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182668534 none O=C(Nc1ccc2c(CN3CCCC3)nn(Cc3c(Cl)cccc3Cl)c2c1)[C@]([O-])([SiH3])C1CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 5, 10, 5, 5, 5, 5, 8, 8, 5, 1, 1, 16, 1, 1, 1, 1, 16, 1, 1, 5, 12, 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, 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, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 4, 4, 17, 17, 17, 17, 17, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 4, 4, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 32, 51, 52, 53, 54, 55, 27, 28, 29, 30, 31] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 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/281161/xco-8058088.67/working/building/ZINC001182668534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182668534 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182668534 Building ZINC001182671343 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182671343 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/384 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc2ccc(c3cncc(OC[C@H](Cc4c[nH]c5ccccc45)NC(=O)[C@@]([O-])([SiH3])C4CC4)c3)cc12) `ZINC001182671343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182671343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 32 is the cov attach 4 32 0 4 32 1 4 32 2 3 32 2 35 to be deleted 36 to be deleted 37 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001182671343 none Cc1[nH]nc2ccc(c3cncc(OC[C@H](Cc4c[nH]c5ccccc45)NC(=O)[C@@]([O-])([SiH3])C4CC4)c3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 29, 29, 29, 29, 29, 17, 7, 5, 2, 5, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 1, 2, 1, 1, 1, 1, 1, 29, 41, 41, 41, 41, 41, 41, 41, 29, 29, 7, 7, 9, 9, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 29, 41] 50 rigid atoms, others: [32, 33, 34, 35, 36, 57, 58, 59, 60, 61, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 385) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc2ccc(c3cncc(OC[C@H](Cc4c[nH]c5ccccc45)NC(=O)[C@]([O-])([SiH3])C4CC4)c3)cc12) `ZINC001182671343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182671343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 32 is the cov attach 4 32 0 4 32 1 4 32 2 3 32 2 35 to be deleted 36 to be deleted 37 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001182671343 none Cc1[nH]nc2ccc(c3cncc(OC[C@H](Cc4c[nH]c5ccccc45)NC(=O)[C@]([O-])([SiH3])C4CC4)c3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 29, 29, 29, 29, 29, 17, 7, 5, 2, 5, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 1, 2, 1, 1, 1, 1, 1, 29, 41, 41, 41, 41, 41, 41, 41, 29, 29, 7, 7, 9, 9, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 29, 41] 50 rigid atoms, others: [32, 33, 34, 35, 36, 57, 58, 59, 60, 61, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182671343 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 Building ZINC001182671343 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182671343 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 384) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1[nH]nc2ccc(c3cncc(OC[C@H](Cc4c[nH]c5ccccc45)NC(=O)[C@@]([O-])([SiH3])C4CC4)c3)cc12) `ZINC001182671343.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182671343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 32 is the cov attach 4 32 0 4 32 1 4 32 2 3 32 2 35 to be deleted 36 to be deleted 37 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001182671343 none Cc1[nH]nc2ccc(c3cncc(OC[C@H](Cc4c[nH]c5ccccc45)NC(=O)[C@@]([O-])([SiH3])C4CC4)c3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 40, 28, 28, 28, 28, 28, 18, 7, 5, 2, 5, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 1, 2, 1, 1, 1, 1, 1, 28, 40, 40, 40, 40, 40, 40, 40, 28, 28, 7, 7, 10, 10, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 28, 40] 50 rigid atoms, others: [32, 33, 34, 35, 36, 57, 58, 59, 60, 61, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 62, 63]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 385) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]nc2ccc(c3cncc(OC[C@H](Cc4c[nH]c5ccccc45)NC(=O)[C@]([O-])([SiH3])C4CC4)c3)cc12) `ZINC001182671343.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182671343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 32 is the cov attach 4 32 0 4 32 1 4 32 2 3 32 2 35 to be deleted 36 to be deleted 37 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001182671343 none Cc1[nH]nc2ccc(c3cncc(OC[C@H](Cc4c[nH]c5ccccc45)NC(=O)[C@]([O-])([SiH3])C4CC4)c3)cc12 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 12, 5, 5, 7, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 29, 29, 29, 29, 29, 17, 7, 5, 2, 5, 5, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 1, 2, 1, 1, 1, 1, 1, 29, 41, 41, 41, 41, 41, 41, 41, 29, 29, 7, 7, 9, 9, 13, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 29, 41] 50 rigid atoms, others: [32, 33, 34, 35, 36, 57, 58, 59, 60, 61, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 62, 63]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182671343 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182671343 Building ZINC001182892152 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182892152 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/386 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(C(=O)OC(C)(C)C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)ncn1) `ZINC001182892152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182892152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182892152 none CC(C)(C)OC(=O)N(C(=O)OC(C)(C)C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 7, 13, 23, 23, 27, 27, 27, 27, 7, 7, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 4, 2, 2, 2, 2, 7] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 387) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(=O)OC(C)(C)C)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)ncn1) `ZINC001182892152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182892152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182892152 none CC(C)(C)OC(=O)N(C(=O)OC(C)(C)C)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 7, 13, 23, 23, 27, 27, 27, 27, 7, 7, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 4, 2, 2, 2, 2, 7] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182892152 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 Building ZINC001182892152 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182892152 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 386) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/386: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N(C(=O)OC(C)(C)C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)ncn1) `ZINC001182892152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182892152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182892152 none CC(C)(C)OC(=O)N(C(=O)OC(C)(C)C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 19, 6, 12, 22, 22, 25, 25, 25, 25, 6, 6, 4, 4, 1, 4, 1, 1, 1, 2, 2, 1, 1, 2, 2, 6, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 25, 25, 25, 25, 25, 25, 25, 25, 25, 6, 4, 2, 2, 2, 2, 6] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 387) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(=O)OC(C)(C)C)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)ncn1) `ZINC001182892152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182892152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182892152 none CC(C)(C)OC(=O)N(C(=O)OC(C)(C)C)c1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 13, 20, 7, 13, 23, 23, 27, 27, 27, 27, 7, 7, 4, 4, 1, 4, 1, 1, 1, 2, 2, 2, 2, 2, 2, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 4, 2, 2, 2, 2, 7] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182892152 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892152 Building ZINC001182892707 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182892707 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/388 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/388' -> `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@@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)C1) `ZINC001182892707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182892707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001182892707 none CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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.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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 29, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [57, 55, 56, 21, 54, 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, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 389) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)C1) `ZINC001182892707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182892707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001182892707 none CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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.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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 29, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [57, 55, 56, 21, 54, 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, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182892707 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 Building ZINC001182892707 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182892707 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 388) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)C2)C1) `ZINC001182892707.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182892707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001182892707 none CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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.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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 15, 15, 15, 15, 15, 15, 3, 1, 5, 1, 1, 1, 2, 2, 1, 1, 2, 2, 15, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 2, 2, 2, 2, 15, 15, 15, 15] 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, 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/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 389) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)C2)C1) `ZINC001182892707.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182892707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001182892707 none CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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.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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7, 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, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 17, 29, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 17, 17, 17, 17] 50 rigid atoms, others: [57, 55, 56, 21, 54, 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, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 58, 59, 60, 61]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182892707 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892707 Building ZINC001182892997 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182892997 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/390 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C[C@H]1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21) `ZINC001182892997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182892997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001182892997 none CCN(CC)C(=O)C[C@H]1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 44, 42, 44, 49, 21, 42, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 21, 21, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 391) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C[C@H]1CC2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21) `ZINC001182892997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182892997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001182892997 none CCN(CC)C(=O)C[C@H]1CC2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 44, 42, 44, 49, 21, 42, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 21, 21, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182892997 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 Building ZINC001182892997 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182892997 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 390) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(CC)C(=O)C[C@H]1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21) `ZINC001182892997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182892997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001182892997 none CCN(CC)C(=O)C[C@H]1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 43, 45, 50, 22, 43, 9, 9, 9, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 50 rigid atoms, others: [54, 55, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 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, 61, 62, 63, 64]) total number of confs: 215 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 391) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C[C@H]1CC2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21) `ZINC001182892997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182892997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001182892997 none CCN(CC)C(=O)C[C@H]1CC2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 44, 42, 44, 49, 21, 42, 8, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 21, 21, 8, 8, 8, 8, 8, 8, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [15, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 220 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182892997 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182892997 Building ZINC001182893004 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893004 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/392 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C[C@@H]1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21) `ZINC001182893004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001182893004 none CCN(CC)C(=O)C[C@@H]1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 40, 45, 50, 24, 40, 10, 10, 10, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [54, 55, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 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, 61, 62, 63, 64]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 393) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C[C@@H]1CC2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21) `ZINC001182893004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001182893004 none CCN(CC)C(=O)C[C@@H]1CC2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 40, 45, 50, 24, 40, 10, 10, 10, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [54, 55, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 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, 61, 62, 63, 64]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182893004 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 Building ZINC001182893004 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893004 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 392) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CCN(CC)C(=O)C[C@@H]1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21) `ZINC001182893004.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001182893004 none CCN(CC)C(=O)C[C@@H]1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 39, 44, 50, 21, 39, 10, 10, 10, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [54, 55, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 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, 61, 62, 63, 64]) total number of confs: 224 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 393) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)C(=O)C[C@@H]1CC2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21) `ZINC001182893004.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001182893004 none CCN(CC)C(=O)C[C@@H]1CC2(CCN(C(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CC2)Oc2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 1, 11, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 40, 45, 50, 24, 40, 10, 10, 10, 10, 10, 10, 10, 5, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [54, 55, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 26, 27, 28, 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, 61, 62, 63, 64]) total number of confs: 218 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182893004 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893004 Building ZINC001182893450 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893450 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/394 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)C1(CN2C(=O)c2ccco2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182893450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182893450 none Cc1ccc2c(c1)C1(CN2C(=O)c2ccco2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 41, 41, 50, 50, 50, 50, 30, 30, 11, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 50, 50, 50, 30, 30, 30, 30, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 395) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)C1(CN2C(=O)c2ccco2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182893450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182893450 none Cc1ccc2c(c1)C1(CN2C(=O)c2ccco2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 41, 41, 50, 50, 50, 50, 30, 30, 11, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 50, 50, 50, 30, 30, 30, 30, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182893450 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 Building ZINC001182893450 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893450 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 394) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1ccc2c(c1)C1(CN2C(=O)c2ccco2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182893450.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182893450 none Cc1ccc2c(c1)C1(CN2C(=O)c2ccco2)CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 28, 28, 39, 39, 50, 50, 50, 50, 28, 28, 9, 1, 15, 1, 1, 1, 2, 2, 1, 1, 2, 2, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 50, 50, 50, 28, 28, 28, 28, 2, 2, 2, 2, 28, 28, 28, 28] 50 rigid atoms, others: [20, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 395) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2c(c1)C1(CN2C(=O)c2ccco2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182893450.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182893450 none Cc1ccc2c(c1)C1(CN2C(=O)c2ccco2)CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens 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, 30, 30, 30, 30, 30, 41, 41, 50, 50, 50, 50, 30, 30, 11, 1, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 50, 50, 50, 30, 30, 30, 30, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [48, 49, 50, 51, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 52, 53, 54, 55]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182893450 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893450 Building ZINC001182893824 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893824 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/396 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1nc(c2cc3cc(O)ccc3[nH]2)c2c1ncnc2NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001182893824 none CC(C)n1nc(c2cc3cc(O)ccc3[nH]2)c2c1ncnc2NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 6, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 30, 15, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 38, 38, 76, 38, 38, 15, 5, 5, 5, 5, 5] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 397) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1nc(c2cc3cc(O)ccc3[nH]2)c2c1ncnc2NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001182893824 none CC(C)n1nc(c2cc3cc(O)ccc3[nH]2)c2c1ncnc2NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 6, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 30, 15, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 38, 38, 76, 38, 38, 15, 5, 5, 5, 5, 5] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182893824 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 Building ZINC001182893824 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182893824 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 396) grep: /scratch/xiaobo/281161/xco-8058088.67/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)n1nc(c2cc3cc(O)ccc3[nH]2)c2c1ncnc2NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182893824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001182893824 none CC(C)n1nc(c2cc3cc(O)ccc3[nH]2)c2c1ncnc2NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 6, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [33, 16, 33, 16, 16, 16, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 16, 16, 16, 16, 16, 5, 5, 1, 5, 1, 1, 1, 4, 4, 1, 1, 4, 4, 33, 33, 33, 33, 33, 33, 33, 37, 37, 74, 37, 37, 16, 5, 4, 4, 4, 4] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 209 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 397) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)n1nc(c2cc3cc(O)ccc3[nH]2)c2c1ncnc2NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182893824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182893824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001182893824 none CC(C)n1nc(c2cc3cc(O)ccc3[nH]2)c2c1ncnc2NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 8, 6, 1, 1, 8, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 3, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 15, 30, 15, 15, 15, 15, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 5, 5, 1, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 38, 38, 76, 38, 38, 15, 5, 5, 5, 5, 5] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 213 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182893824 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182893824 Building ZINC001182894654 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182894654 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/398 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 12, 12, 12, 12, 12, 21, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 21, 21, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/399 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/399' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/400 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/400' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 401) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894654 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 Building ZINC001182894654 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182894654 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 398) grep: /scratch/xiaobo/281161/xco-8058088.67/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(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 12, 12, 12, 12, 12, 21, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 21, 21, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 399) grep: /scratch/xiaobo/281161/xco-8058088.67/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(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 12, 12, 12, 12, 12, 21, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 21, 21, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 400) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 401) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894654 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 Building ZINC001182894654 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182894654 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 398) grep: /scratch/xiaobo/281161/xco-8058088.67/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(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 12, 12, 12, 12, 12, 21, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 21, 21, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 399) grep: /scratch/xiaobo/281161/xco-8058088.67/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(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 12, 12, 12, 12, 12, 21, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 21, 21, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 400) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 401) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894654 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 Building ZINC001182894654 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182894654 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 398) grep: /scratch/xiaobo/281161/xco-8058088.67/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(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 12, 12, 12, 12, 12, 21, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 21, 21, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 399) grep: /scratch/xiaobo/281161/xco-8058088.67/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(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 12, 12, 12, 12, 12, 21, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 21, 21, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 400) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/400: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 401) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182894654.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182894654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001182894654 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 11, 11, 11, 11, 11, 18, 22, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 18, 18, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 1, 1, 1, 1] 50 rigid atoms, others: [32, 1, 59, 33, 60, 61, 62, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894654 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894654 Building ZINC001182894902 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182894902 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 402) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh Failed to generate 3D embedding in both batch and single-runs Skipping ZINC001182894902 0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 `0' -> `0.failed' Finished preparing ZINC001182894902 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Found failed protomers Marking ZINC001182894902 as failed `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902' -> `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902' Building ZINC001182894902 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182894902 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 402) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh Failed to generate 3D embedding in both batch and single-runs Skipping ZINC001182894902 0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 `0' -> `0.failed' Finished preparing ZINC001182894902 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Found failed protomers Marking ZINC001182894902 as failed `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894902' -> `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902' Building ZINC001182894904 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182894904 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 404) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182894904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182894904 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 9, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 405) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182894904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182894904 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 3, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 11, 11, 11, 11] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894904 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 Building ZINC001182894904 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182894904 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 404) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182894904.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182894904 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 23, 9, 23, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 9, 1, 1, 1, 3, 3, 1, 1, 3, 3, 9, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 9, 9, 9, 9] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 405) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182894904.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001182894904 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 3, 10, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 2, 11, 11, 11, 11] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 111 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894904 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894904 Building ZINC001182894910 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182894910 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/406 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/407 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/407' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 408) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 409) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894910 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 Building ZINC001182894910 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182894910 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 406) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 7, 7, 7, 7, 7, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 407) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 20, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 7, 7, 7, 3, 2, 2, 2, 2, 19, 19, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 408) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 409) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894910 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 Building ZINC001182894910 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182894910 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 406) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 7, 7, 7, 7, 7, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 407) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 20, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 7, 7, 7, 3, 2, 2, 2, 2, 19, 19, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 408) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 409) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894910 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 Building ZINC001182894910 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182894910 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 406) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 7, 7, 7, 7, 7, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 407) grep: /scratch/xiaobo/281161/xco-8058088.67/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: Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 7, 7, 20, 33, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 33, 33, 7, 7, 7, 7, 7, 3, 2, 2, 2, 2, 19, 19, 33, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 408) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 409) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)n1) `ZINC001182894910.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182894910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001182894910 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)n(C[C@H]2CC[N@@](Cc3ccccc3)CC2)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.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 8, 5, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 32, 32, 8, 8, 8, 8, 8, 3, 2, 2, 2, 2, 19, 19, 32, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 32] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182894910 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182894910 Building ZINC001182895740 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182895740 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 410) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182895740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182895740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182895740 none CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(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.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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 26, 37, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 26, 26, 26, 26] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 411) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182895740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182895740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182895740 none CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(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.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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 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] 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] 0 hydrogens need rotated 50 conformations 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, 30, 42, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 2, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 30, 30, 30, 30] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182895740 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 Building ZINC001182895740 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182895740 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 410) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182895740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182895740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182895740 none CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(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.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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 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] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 37, 26, 37, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 1, 18, 1, 1, 1, 3, 3, 1, 1, 3, 3, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 3, 3, 3, 3, 26, 26, 26, 26] 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]) total number of confs: 123 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 411) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)CC2) `ZINC001182895740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182895740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182895740 none CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(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.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', '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'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 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] 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] 0 hydrogens need rotated 50 conformations 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, 30, 42, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 12, 2, 17, 1, 1, 1, 2, 2, 1, 1, 2, 2, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 2, 2, 2, 2, 30, 30, 30, 30] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182895740 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182895740 Building ZINC001182896197 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896197 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 412) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182896197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182896197 none O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 16, 16, 10, 10, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 49, 49, 50, 50, 50, 50, 16, 16, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 34, 51, 52, 53, 54, 24, 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, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 413) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182896197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182896197 none O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 14, 14, 10, 10, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 6, 6, 6, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 46, 46, 50, 50, 50, 50, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [32, 33, 34, 51, 52, 53, 54, 24, 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, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182896197 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 Building ZINC001182896197 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896197 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 412) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182896197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182896197 none O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 4, 10, 16, 16, 10, 10, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 4, 4, 4, 2, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 16, 16, 49, 49, 50, 50, 50, 50, 16, 16, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [32, 33, 34, 51, 52, 53, 54, 24, 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, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 413) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182896197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001182896197 none O=C(c1ccc(/C=C/c2n[nH]c3ccccc23)cc1)N1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 14, 14, 10, 10, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 6, 6, 6, 2, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 14, 46, 46, 50, 50, 50, 50, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [32, 33, 34, 51, 52, 53, 54, 24, 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, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 56, 57, 58]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182896197 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896197 Building ZINC001182896553 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896553 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 414) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)ccc32)cs1) `ZINC001182896553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182896553 none Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)ccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 13, 13, 50, 50, 50, 50, 50, 40, 40, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 12, 13, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 415) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)ccc32)cs1) `ZINC001182896553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182896553 none Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)ccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 13, 13, 50, 50, 50, 50, 50, 40, 40, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 12, 13, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182896553 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 Building ZINC001182896553 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896553 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 414) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)ccc32)cs1) `ZINC001182896553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182896553 none Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@@]([O-])([SiH3])c4ccc(Cl)cc4)ccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 13, 13, 50, 50, 50, 50, 50, 40, 40, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 12, 13, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 415) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)ccc32)cs1) `ZINC001182896553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001182896553 none Cc1nc(CN2C(=O)C3(CCOCC3)c3cc(NC(=O)[C@]([O-])([SiH3])c4ccc(Cl)cc4)ccc32)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 11, 13, 13, 50, 50, 50, 50, 50, 40, 40, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 2, 2, 12, 13, 50] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182896553 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896553 Building ZINC001182896600 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896600 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 416) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cccc(F)c2N)CC1) `ZINC001182896600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182896600 none CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cccc(F)c2N)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', '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.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 17, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 9, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 2, 2, 2, 2, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 96 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 417) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cccc(F)c2N)CC1) `ZINC001182896600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182896600 none CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cccc(F)c2N)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', '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.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 34, 16, 7, 16, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 5, 9, 9, 9, 9, 9, 9, 9, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 2, 2, 2, 2, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182896600 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 Building ZINC001182896600 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182896600 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 416) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cccc(F)c2N)CC1) `ZINC001182896600.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182896600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182896600 none CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)c2cccc(F)c2N)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', '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.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 7, 17, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 5, 9, 9, 9, 9, 9, 9, 9, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 7, 7, 7, 7, 2, 2, 2, 2, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [12, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 96 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 417) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cccc(F)c2N)CC1) `ZINC001182896600.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182896600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182896600 none CC(C)(C)OC(=O)N1CCC(N(C(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)c2cccc(F)c2N)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', '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.ar', 'F', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 15, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 34, 16, 7, 16, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 2, 2, 1, 2, 2, 2, 5, 9, 9, 9, 9, 9, 9, 9, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 7, 7, 7, 2, 2, 2, 2, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 98 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182896600 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182896600 Building ZINC001182897067 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897067 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/418 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 5, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/419 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/419' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 420) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 5, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 421) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897067 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 Building ZINC001182897067 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897067 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 418) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 24, 24, 24, 24, 24, 8, 7, 7, 5, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 24, 24, 24, 24, 7, 7, 7, 3, 2, 2, 2, 2, 24, 24, 24, 24] 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, 58, 59]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 419) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 48, 24, 24, 24, 24, 24, 8, 7, 7, 5, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 24, 24, 24, 24, 7, 7, 7, 3, 2, 2, 2, 2, 24, 24, 24, 24] 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, 58, 59]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 420) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 5, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 421) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897067 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 Building ZINC001182897067 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897067 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 418) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 24, 24, 24, 24, 24, 8, 7, 7, 5, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 24, 24, 24, 24, 7, 7, 7, 3, 2, 2, 2, 2, 24, 24, 24, 24] 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, 58, 59]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 419) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 48, 24, 24, 24, 24, 24, 8, 7, 7, 5, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 24, 24, 24, 24, 7, 7, 7, 3, 2, 2, 2, 2, 24, 24, 24, 24] 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, 58, 59]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 420) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 5, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 421) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897067 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 Building ZINC001182897067 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897067 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 418) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 24, 24, 24, 24, 24, 8, 7, 7, 5, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 24, 24, 24, 24, 7, 7, 7, 3, 2, 2, 2, 2, 24, 24, 24, 24] 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, 58, 59]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 419) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 48, 24, 24, 24, 24, 24, 8, 7, 7, 5, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 24, 24, 24, 24, 7, 7, 7, 3, 2, 2, 2, 2, 24, 24, 24, 24] 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, 58, 59]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 420) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 5, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 421) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1) `ZINC001182897067.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897067 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2ccc(Cl)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 36, 47, 23, 23, 23, 23, 23, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 2, 1, 1, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 23, 23, 23, 23, 6, 6, 6, 3, 2, 2, 2, 2, 23, 23, 23, 23] 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, 58, 59]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897067 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897067 Building ZINC001182897395 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897395 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/422 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/423 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/423' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 424) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 425) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897395 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 Building ZINC001182897395 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897395 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 422) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 33, 45, 21, 21, 21, 21, 21, 21, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 21, 21, 21, 21, 21, 21, 8, 8, 2, 2, 2, 2, 2, 8, 8, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 423) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 33, 45, 21, 21, 21, 21, 21, 21, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 21, 21, 21, 21, 21, 21, 8, 8, 2, 2, 2, 2, 2, 8, 8, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 424) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 425) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897395 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 Building ZINC001182897395 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897395 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 422) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 33, 45, 21, 21, 21, 21, 21, 21, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 21, 21, 21, 21, 21, 21, 8, 8, 2, 2, 2, 2, 2, 8, 8, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 423) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 33, 45, 21, 21, 21, 21, 21, 21, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 21, 21, 21, 21, 21, 21, 8, 8, 2, 2, 2, 2, 2, 8, 8, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 424) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 425) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897395 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 Building ZINC001182897395 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897395 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 422) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 33, 45, 21, 21, 21, 21, 21, 21, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 21, 21, 21, 21, 21, 21, 8, 8, 2, 2, 2, 2, 2, 8, 8, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 423) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 33, 45, 21, 21, 21, 21, 21, 21, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 21, 21, 21, 21, 21, 21, 8, 8, 2, 2, 2, 2, 2, 8, 8, 21, 21] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 424) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 425) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897395.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897395 none CC(C)(C)OC(=O)N[C@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 31, 45, 20, 20, 20, 20, 20, 20, 8, 4, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 20, 20, 20, 20, 20, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 20, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897395 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897395 Building ZINC001182897398 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897398 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/426 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/427 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/427' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 428) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 429) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897398 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 Building ZINC001182897398 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897398 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 426) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 427) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 428) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 429) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897398 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 Building ZINC001182897398 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897398 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 426) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 427) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 428) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 429) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897398 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 Building ZINC001182897398 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001182897398 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 426) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 427) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 8, 8, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 22, 22, 22, 22, 22, 22, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 22] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 428) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 429) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)cc2)C1) `ZINC001182897398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001182897398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001182897398 none CC(C)(C)OC(=O)N[C@@H]1CCCN(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)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', 'H', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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, 7, 5, 5, 5, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 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, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 22, 22, 22, 22, 22, 22, 4, 2, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 2, 2, 8, 8, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 22, 22, 22, 22, 22, 20, 8, 8, 2, 2, 2, 2, 2, 8, 8, 22, 20] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182897398 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182897398 Building ZINC001182898153 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182898153 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 430) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc2cccc(F)c2c(=O)n1c1ccccc1) `ZINC001182898153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182898153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001182898153 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc2cccc(F)c2c(=O)n1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 6, 13, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 33, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 47, 47, 45, 47, 47, 25, 25, 25, 25, 25, 6, 4, 4, 4, 4, 43, 43, 43, 47, 47, 45, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 431) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc2cccc(F)c2c(=O)n1c1ccccc1) `ZINC001182898153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182898153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001182898153 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc2cccc(F)c2c(=O)n1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 13, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 34, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 6, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182898153 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 Building ZINC001182898153 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182898153 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 430) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc2cccc(F)c2c(=O)n1c1ccccc1) `ZINC001182898153.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182898153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001182898153 none CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc2cccc(F)c2c(=O)n1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 13, 6, 13, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 33, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 47, 47, 45, 47, 47, 25, 25, 25, 25, 25, 6, 4, 4, 4, 4, 43, 43, 43, 47, 47, 45, 47, 47] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 431) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc2cccc(F)c2c(=O)n1c1ccccc1) `ZINC001182898153.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182898153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001182898153 none CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1)c1nc2cccc(F)c2c(=O)n1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', '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.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 1, 8, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 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, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 13, 6, 1, 6, 1, 1, 1, 4, 4, 1, 1, 4, 4, 13, 34, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 27, 27, 27, 27, 27, 6, 4, 4, 4, 4, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [5, 7, 8, 9] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182898153 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898153 Building ZINC001182898939 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182898939 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 432) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182898939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182898939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182898939 none O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 4, 4, 12, 14, 14, 12, 14, 14, 14, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 34, 34, 34, 34, 34, 34, 34, 12, 12, 14, 14, 28, 14, 14, 2, 2, 2, 2, 2] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 433) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182898939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182898939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182898939 none O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 5, 5, 12, 13, 13, 12, 13, 13, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 35, 35, 35, 35, 35, 35, 35, 12, 12, 13, 13, 26, 13, 13, 3, 3, 3, 3, 3] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182898939 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 Building ZINC001182898939 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182898939 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 432) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182898939.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182898939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182898939 none O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 11, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 2, 4, 4, 12, 14, 14, 12, 14, 14, 14, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 11, 34, 34, 34, 34, 34, 34, 34, 12, 12, 14, 14, 28, 14, 14, 2, 2, 2, 2, 2] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 433) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1) `ZINC001182898939.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182898939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001182898939 none O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])c1ccc(Cl)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 3, 5, 5, 12, 13, 13, 12, 13, 13, 13, 3, 1, 3, 1, 1, 1, 3, 3, 1, 1, 3, 3, 10, 35, 35, 35, 35, 35, 35, 35, 12, 12, 13, 13, 26, 13, 13, 3, 3, 3, 3, 3] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 141 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182898939 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182898939 Building ZINC001182900380 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182900380 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 434) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001182900380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182900380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001182900380 none COc1cccc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 19, 19, 19, 19, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 17, 17, 24, 25, 25, 25, 8, 8, 19, 23, 23, 23, 19, 19, 19, 4, 3, 3, 3, 3, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 435) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001182900380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182900380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001182900380 none COc1cccc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 14, 14, 20, 20, 20, 20, 8, 8, 19, 22, 22, 22, 19, 19, 19, 4, 3, 3, 3, 3, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182900380 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 Building ZINC001182900380 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001182900380 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 434) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001182900380.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001182900380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001182900380 none COc1cccc(C2(NC(=O)[C@@]([O-])([SiH3])c3ccc(Cl)cc3)CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 19, 19, 19, 19, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 1, 3, 3, 8, 8, 8, 8, 17, 17, 24, 25, 25, 25, 8, 8, 19, 23, 23, 23, 19, 19, 19, 4, 3, 3, 3, 3, 8, 8, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 8, 8, 8, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 100 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 435) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CCN(C(=O)OC(C)(C)C)CC2)c1) `ZINC001182900380.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001182900380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001182900380 none COc1cccc(C2(NC(=O)[C@]([O-])([SiH3])c3ccc(Cl)cc3)CCN(C(=O)OC(C)(C)C)CC2)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'N.am', 'C.2', 'O.2', 'O.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 8, 1, 11, 12, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 8, 4, 4, 1, 4, 1, 1, 1, 3, 3, 3, 3, 3, 3, 8, 8, 8, 8, 14, 14, 20, 20, 20, 20, 8, 8, 19, 22, 22, 22, 19, 19, 19, 4, 3, 3, 3, 3, 8, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 8, 8, 8, 8, 19] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 81 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001182900380 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001182900380 Building ZINC001183095717 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183095717 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 436) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)n(c3ccccc3)n2)cc1) `ZINC001183095717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183095717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183095717 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 18, 18, 26, 26, 8, 8, 8, 5, 3, 1, 3, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 8, 5, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 101 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 437) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)n(c3ccccc3)n2)cc1) `ZINC001183095717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183095717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183095717 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 27, 27, 8, 8, 8, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 8, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183095717 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 Building ZINC001183095717 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183095717 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 436) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)n(c3ccccc3)n2)cc1) `ZINC001183095717.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183095717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183095717 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 18, 18, 26, 26, 8, 8, 8, 5, 3, 1, 3, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26, 26, 26, 26, 26, 26, 8, 5, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 26] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 101 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 437) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)n(c3ccccc3)n2)cc1) `ZINC001183095717.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183095717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001183095717 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 27, 27, 8, 8, 8, 4, 2, 1, 2, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 8, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 118 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183095717 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095717 Building ZINC001183095965 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183095965 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 438) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183095965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183095965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001183095965 none O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 32, 32, 32, 32, 32, 32, 4, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 15, 15, 32, 32, 32, 32, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 439) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183095965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183095965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001183095965 none O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 16, 32, 32, 27, 32, 32, 32, 4, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 16, 16, 32, 32, 32, 32, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183095965 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 Building ZINC001183095965 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183095965 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 438) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183095965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183095965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001183095965 none O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 15, 32, 32, 32, 32, 32, 32, 4, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 15, 15, 32, 32, 32, 32, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 439) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183095965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183095965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001183095965 none O=C(Nc1csc(Cc2cccc(Br)c2)n1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 4, 4, 4, 16, 32, 32, 27, 32, 32, 32, 4, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 16, 16, 32, 32, 32, 32, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183095965 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183095965 Building ZINC001183096080 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096080 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/440 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/441 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/441' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 442) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 443) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096080 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 Building ZINC001183096080 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096080 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 440) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 24, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 31, 26, 15, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 26, 26, 24, 23, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 441) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 24, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 31, 26, 15, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 26, 26, 24, 23, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 442) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 443) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096080 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 Building ZINC001183096080 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096080 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 440) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 24, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 31, 26, 15, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 26, 26, 24, 23, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 441) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 24, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 31, 26, 15, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 26, 26, 24, 23, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 442) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 443) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096080 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 Building ZINC001183096080 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096080 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 440) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 24, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 31, 26, 15, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 26, 26, 24, 23, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 441) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 24, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 31, 26, 15, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 26, 26, 26, 26, 26, 26, 31, 32, 32, 31, 32, 32, 31, 31, 31, 31, 31, 26, 26, 24, 23, 6, 6, 10, 10, 10, 10, 10] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 442) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 443) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096080.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 67 natoms 66 natoms 65 natoms 64 names: ZINC001183096080 none O=C(N1CCC2(CN(C(c3ccccc3)c3ccccc3)C2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 21, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 16, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 23, 23, 23, 23, 23, 23, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 23, 23, 20, 22, 7, 7, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096080 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096080 Building ZINC001183096097 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096097 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/444 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/445 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/445' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 446) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 447) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096097 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 Building ZINC001183096097 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096097 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 444) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 29, 32, 32, 29, 32, 32, 10, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 29, 29, 32, 32, 29, 32, 32, 10, 10, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 445) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 29, 32, 32, 29, 32, 32, 10, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 29, 29, 32, 32, 29, 32, 32, 10, 10, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 446) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 447) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096097 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 Building ZINC001183096097 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096097 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 444) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 29, 32, 32, 29, 32, 32, 10, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 29, 29, 32, 32, 29, 32, 32, 10, 10, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 445) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 29, 32, 32, 29, 32, 32, 10, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 29, 29, 32, 32, 29, 32, 32, 10, 10, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 446) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 447) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096097 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 Building ZINC001183096097 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096097 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 444) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 29, 32, 32, 29, 32, 32, 10, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 29, 29, 32, 32, 29, 32, 32, 10, 10, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 445) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 29, 32, 32, 29, 32, 32, 10, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 29, 29, 32, 32, 29, 32, 32, 10, 10, 5, 5, 9, 9, 9, 9, 9] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 148 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 446) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 447) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096097.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096097 none O=C(N(Cc1ccccc1)[C@@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 5, 5, 5, 5, 5, 5, 6, 9, 9, 9, 9, 9, 24, 30, 30, 24, 30, 30, 9, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 24, 24, 30, 30, 24, 30, 30, 9, 9, 5, 5, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096097 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096097 Building ZINC001183096100 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096100 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/448 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/449 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/449' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 450) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 451) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096100 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 Building ZINC001183096100 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096100 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 448) grep: /scratch/xiaobo/281161/xco-8058088.67/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(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 26, 33, 33, 30, 33, 33, 8, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 26, 26, 33, 33, 33, 33, 33, 8, 8, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 158 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 449) grep: /scratch/xiaobo/281161/xco-8058088.67/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(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 26, 33, 33, 30, 33, 33, 8, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 26, 26, 33, 33, 33, 33, 33, 8, 8, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 158 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 450) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 451) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096100 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 Building ZINC001183096100 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096100 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 448) grep: /scratch/xiaobo/281161/xco-8058088.67/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(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 26, 33, 33, 30, 33, 33, 8, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 26, 26, 33, 33, 33, 33, 33, 8, 8, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 158 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 449) grep: /scratch/xiaobo/281161/xco-8058088.67/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(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 26, 33, 33, 30, 33, 33, 8, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 26, 26, 33, 33, 33, 33, 33, 8, 8, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 158 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 450) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 451) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096100 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 Building ZINC001183096100 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183096100 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 448) grep: /scratch/xiaobo/281161/xco-8058088.67/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(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 26, 33, 33, 30, 33, 33, 8, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 26, 26, 33, 33, 33, 33, 33, 8, 8, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 158 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 449) grep: /scratch/xiaobo/281161/xco-8058088.67/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(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 8, 8, 8, 8, 8, 26, 33, 33, 30, 33, 33, 8, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6, 6, 6, 6, 6, 8, 8, 8, 8, 26, 26, 33, 33, 33, 33, 33, 8, 8, 7, 7, 8, 8, 8, 8, 8] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 158 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 450) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 451) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096100.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183096100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 66 natoms 65 natoms 64 natoms 63 names: ZINC001183096100 none O=C(N(Cc1ccccc1)[C@H]1CCN(Cc2ccccc2)C1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 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', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 5, 6, 6, 6, 6, 6, 6, 5, 9, 9, 9, 9, 9, 26, 32, 32, 28, 32, 32, 9, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 26, 26, 32, 32, 32, 32, 32, 9, 9, 5, 5, 6, 6, 6, 6, 6] 50 rigid atoms, others: [24, 1, 25, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 155 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096100 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096100 Building ZINC001183096118 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096118 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 452) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001183096118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001183096118 none CC(C)(C)CN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 13, 13, 29, 30, 30, 30, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 453) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001183096118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001183096118 none CC(C)(C)CN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 14, 14, 26, 27, 27, 27, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096118 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 Building ZINC001183096118 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096118 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 452) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001183096118.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001183096118 none CC(C)(C)CN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 5, 5, 5, 13, 13, 29, 30, 30, 30, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 79 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 453) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)CN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)C1CCN(C(=O)OC(C)(C)C)CC1) `ZINC001183096118.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 73 natoms 72 natoms 71 natoms 70 names: ZINC001183096118 none CC(C)(C)CN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)C1CCN(C(=O)OC(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 1, 3, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 6, 6, 6, 6, 14, 14, 26, 27, 27, 27, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 6, 6, 6] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 80 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096118 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096118 Building ZINC001183096219 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096219 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 454) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCSc1cc(C(F)(F)F)nc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001183096219 none O=C(NCCSc1cc(C(F)(F)F)nc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 8, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 8, 8, 37, 37, 37, 37, 37, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 33, 20, 21, 22] set([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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 455) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCSc1cc(C(F)(F)F)nc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001183096219 none O=C(NCCSc1cc(C(F)(F)F)nc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 8, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 8, 8, 37, 37, 37, 37, 37, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 33, 20, 21, 22] set([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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096219 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 Building ZINC001183096219 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096219 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 454) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCSc1cc(C(F)(F)F)nc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001183096219 none O=C(NCCSc1cc(C(F)(F)F)nc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 8, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 8, 8, 37, 37, 37, 37, 37, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 33, 20, 21, 22] set([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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 455) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCSc1cc(C(F)(F)F)nc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001183096219 none O=C(NCCSc1cc(C(F)(F)F)nc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 14, 1, 1, 1, 5, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 8, 19, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 5, 5, 8, 8, 37, 37, 37, 37, 37, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 33, 20, 21, 22] set([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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096219 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096219 Building ZINC001183096539 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096539 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 456) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001183096539 none O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 6, 6, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 457) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001183096539 none O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 7, 7, 10, 10, 10, 10, 10] 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]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096539 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 Building ZINC001183096539 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096539 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 456) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096539.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001183096539 none O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 4, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 4, 4, 4, 4, 6, 6, 7, 7, 7, 7, 7] 50 rigid atoms, others: [24, 1, 26, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 457) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183096539.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001183096539 none O=C(N1CCN(C2=Nc3ccccc3Oc3ccc(Cl)cc32)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 8, 1, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 1, 1, 1, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6, 7, 7, 10, 10, 10, 10, 10] 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]) total number of confs: 64 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096539 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096539 Building ZINC001183096965 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096965 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 458) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1OC) `ZINC001183096965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183096965 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 29, 26, 26, 26, 17, 17, 3, 3, 3, 3, 1, 2, 2, 5, 5, 5, 5, 5, 17, 29, 29, 29] 50 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 459) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1OC) `ZINC001183096965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183096965 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 29, 27, 27, 27, 17, 17, 3, 3, 3, 3, 1, 3, 3, 6, 6, 6, 6, 6, 17, 29, 29, 29] 50 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096965 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 Building ZINC001183096965 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183096965 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 458) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1OC) `ZINC001183096965.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183096965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183096965 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 29, 26, 26, 26, 17, 17, 3, 3, 3, 3, 1, 2, 2, 5, 5, 5, 5, 5, 17, 29, 29, 29] 50 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 459) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1OC) `ZINC001183096965.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183096965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001183096965 none COc1ccc(C(=O)c2oc3ccccc3c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1OC NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 1, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 17, 17, 17, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 29, 27, 27, 27, 17, 17, 3, 3, 3, 3, 1, 3, 3, 6, 6, 6, 6, 6, 17, 29, 29, 29] 50 rigid atoms, others: [46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183096965 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183096965 Building ZINC001183097014 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097014 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 460) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC[C@@]2(CCCCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001183097014 none CC(C)(C)OC(=O)N1CCCC[C@@]2(CCCCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 26, 26, 20, 11, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 11, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 18, 18, 18, 18, 18, 11, 11, 11, 11] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 111 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 461) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC[C@@]2(CCCCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001183097014 none CC(C)(C)OC(=O)N1CCCC[C@@]2(CCCCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 2, 18, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 14, 14, 14, 14, 14, 18, 18, 18, 18] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 107 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097014 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 Building ZINC001183097014 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097014 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 460) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC[C@@]2(CCCCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097014.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001183097014 none CC(C)(C)OC(=O)N1CCCC[C@@]2(CCCCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 25, 26, 26, 20, 11, 20, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 11, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 11, 26, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 18, 18, 18, 18, 18, 11, 11, 11, 11] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 111 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 461) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC[C@@]2(CCCCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097014.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001183097014 none CC(C)(C)OC(=O)N1CCCC[C@@]2(CCCCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 2, 18, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 18, 18, 29, 29, 29, 29, 29, 29, 29, 29, 29, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 7, 7, 14, 14, 14, 14, 14, 18, 18, 18, 18] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 107 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097014 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097014 Building ZINC001183097020 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097020 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 462) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC[C@]2(CCCCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001183097020 none CC(C)(C)OC(=O)N1CCCC[C@]2(CCCCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 21, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 3, 13, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 14, 14, 14, 14, 14, 13, 13, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 103 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 463) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC[C@]2(CCCCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001183097020 none CC(C)(C)OC(=O)N1CCCC[C@]2(CCCCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 3, 13, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 104 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097020 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 Building ZINC001183097020 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097020 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 462) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC[C@]2(CCCCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001183097020 none CC(C)(C)OC(=O)N1CCCC[C@]2(CCCCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 21, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 11, 3, 13, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 14, 14, 14, 14, 14, 13, 13, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 103 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 463) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC[C@]2(CCCCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001183097020 none CC(C)(C)OC(=O)N1CCCC[C@]2(CCCCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 22, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 12, 3, 13, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 104 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097020 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097020 Building ZINC001183097076 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097076 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 464) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 72 natoms 71 natoms 70 natoms 69 names: ZINC001183097076 none CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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.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.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 20, 12, 20, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 1, 10, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 465) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 72 natoms 71 natoms 70 natoms 69 names: ZINC001183097076 none CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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.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.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 21, 13, 21, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 8, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097076 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 Building ZINC001183097076 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097076 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 464) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 72 natoms 71 natoms 70 natoms 69 names: ZINC001183097076 none CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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.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.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 20, 12, 20, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 1, 10, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 465) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)C2)C1) `ZINC001183097076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 72 natoms 71 natoms 70 natoms 69 names: ZINC001183097076 none CC(C)(C)OC(=O)N1C[C@H](c2ccccc2)[C@@]2(CCN(C(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)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.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.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 21, 13, 21, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 8, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 26, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68]) total number of confs: 96 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097076 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097076 Building ZINC001183097797 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183097797 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/466 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/467 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/467' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 468) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 469) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097797 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 Building ZINC001183097797 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183097797 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 466) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 11, 12, 12, 12, 12, 12, 20, 20, 30, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 12, 12, 3, 3, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 198 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 467) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 11, 12, 12, 12, 12, 12, 20, 20, 30, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 12, 12, 3, 3, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 198 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 468) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 469) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097797 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 Building ZINC001183097797 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183097797 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 466) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 11, 12, 12, 12, 12, 12, 20, 20, 30, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 12, 12, 3, 3, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 198 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 467) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 11, 12, 12, 12, 12, 12, 20, 20, 30, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 12, 12, 3, 3, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 198 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 468) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 469) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097797 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 Building ZINC001183097797 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183097797 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 466) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 11, 12, 12, 12, 12, 12, 20, 20, 30, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 12, 12, 3, 3, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 198 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 467) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 1, 11, 12, 12, 12, 12, 12, 20, 20, 30, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 12, 12, 12, 12, 3, 3, 4, 4, 4, 4, 4] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 198 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 468) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 469) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097797.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183097797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183097797 none O=C(N1CCCN(CCOC(c2ccccc2)c2ccccc2)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', '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.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 10, 18, 19, 32, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 10, 18, 18, 19, 19, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 10, 10, 10, 10, 4, 4, 5, 5, 5, 5, 5] 50 rigid atoms, others: [1, 26, 27, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69]) total number of confs: 174 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097797 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097797 Building ZINC001183097808 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097808 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 470) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183097808 none O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 471) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183097808 none O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 9, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 20, 20, 20, 20, 13, 13, 13, 13, 9, 9, 17, 17, 17, 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]) total number of confs: 80 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097808 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 Building ZINC001183097808 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183097808 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 470) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097808.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183097808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183097808 none O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 1, 1, 1, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 9, 9, 9, 9, 15, 15, 15, 15, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15] 50 rigid atoms, others: [21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 67 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 471) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183097808.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183097808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183097808 none O=C(N1CCC(n2c3ccccc3nc2C(F)(F)F)CC1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 9, 13, 13, 13, 13, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 1, 1, 1, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 13, 13, 13, 13, 13, 20, 20, 20, 20, 13, 13, 13, 13, 9, 9, 17, 17, 17, 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]) total number of confs: 80 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183097808 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183097808 Building ZINC001183098162 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098162 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 472) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001183098162 none Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 51, 9, 9, 3, 4, 4, 6, 6, 6, 6, 6] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 473) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001183098162 none Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 3, 3, 17, 17, 19, 17, 25, 17, 17, 25, 19, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 52, 8, 8, 3, 3, 3, 5, 5, 5, 5, 5] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098162 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 Building ZINC001183098162 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098162 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 472) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098162.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001183098162 none Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 3, 3, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 3, 3, 1, 3, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 9, 9, 9, 9, 51, 9, 9, 3, 4, 4, 6, 6, 6, 6, 6] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 473) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098162.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001183098162 none Cc1cc(C(O)(C(F)(F)F)C(F)(F)F)ccc1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 15, 15, 15, 5, 15, 15, 15, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 8, 8, 3, 3, 17, 17, 19, 17, 25, 17, 17, 25, 19, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 8, 8, 8, 8, 52, 8, 8, 3, 3, 3, 5, 5, 5, 5, 5] 150 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098162 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098162 Building ZINC001183098362 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098362 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 474) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1ccccc1)(c1ccccc1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001183098362 none COC(c1ccccc1)(c1ccccc1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 18, 12, 18, 19, 19, 18, 19, 19, 18, 23, 23, 18, 23, 23, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 19, 19, 18, 19, 19, 23, 23, 18, 23, 23, 12, 12, 12, 12, 12, 12, 5, 5, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 127 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 475) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1ccccc1)(c1ccccc1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001183098362 none COC(c1ccccc1)(c1ccccc1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 17, 19, 19, 17, 19, 19, 17, 21, 21, 17, 21, 21, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 19, 19, 17, 19, 19, 21, 21, 17, 21, 21, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 144 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098362 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 Building ZINC001183098362 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098362 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 474) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1ccccc1)(c1ccccc1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001183098362 none COC(c1ccccc1)(c1ccccc1)[C@@H]1CCCN1C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 18, 12, 18, 19, 19, 18, 19, 19, 18, 23, 23, 18, 23, 23, 12, 12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 26, 26, 26, 19, 19, 18, 19, 19, 23, 23, 18, 23, 23, 12, 12, 12, 12, 12, 12, 5, 5, 12, 12, 12, 12, 12] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 127 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 475) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1ccccc1)(c1ccccc1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183098362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 65 natoms 64 natoms 63 natoms 62 names: ZINC001183098362 none COC(c1ccccc1)(c1ccccc1)[C@@H]1CCCN1C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 9, 17, 19, 19, 17, 19, 19, 17, 21, 21, 17, 21, 21, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 19, 19, 17, 19, 19, 21, 21, 17, 21, 21, 9, 9, 9, 9, 9, 9, 9, 9, 19, 19, 19, 19, 19] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 144 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098362 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098362 Building ZINC001183098800 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098800 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 476) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183098800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098800 none CC(C)(C)OC(=O)N1CCC2(CC[C@@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 477) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183098800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098800 none CC(C)(C)OC(=O)N1CCC2(CC[C@@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098800 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 Building ZINC001183098800 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098800 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 476) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183098800.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098800 none CC(C)(C)OC(=O)N1CCC2(CC[C@@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 7, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 7, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 84 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 477) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183098800.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098800 none CC(C)(C)OC(=O)N1CCC2(CC[C@@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 6, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 6, 6] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098800 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098800 Building ZINC001183098801 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098801 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 478) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183098801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098801 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 21, 11, 5, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 479) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183098801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098801 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 51 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098801 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 Building ZINC001183098801 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098801 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 478) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183098801.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098801 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 21, 11, 5, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 479) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183098801.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183098801 none CC(C)(C)OC(=O)N1CCC2(CC[C@H](C(F)(F)F)N2C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 7, 5, 15, 15, 15, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 6, 3, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 7, 7, 7, 7, 7, 3, 3, 3, 3] 50 rigid atoms, others: [24, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 51 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098801 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098801 Building ZINC001183098967 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098967 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 480) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1nc2cc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)ccc2s1) `ZINC001183098967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001183098967 none CC(C)(C)OC(=O)Nc1nc2cc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)ccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 29, 29, 14, 14, 14, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 12, 2, 2, 2, 5, 5, 5, 5, 5, 12, 12] 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 481) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1nc2cc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)ccc2s1) `ZINC001183098967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001183098967 none CC(C)(C)OC(=O)Nc1nc2cc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)ccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 28, 28, 14, 14, 14, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 12, 2, 2, 2, 5, 5, 5, 5, 5, 12, 12] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098967 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 Building ZINC001183098967 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183098967 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 480) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1nc2cc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)ccc2s1) `ZINC001183098967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183098967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001183098967 none CC(C)(C)OC(=O)Nc1nc2cc(NC(=O)[C@@]([O-])([SiH3])Cc3c[nH]c4ccccc34)ccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 27, 29, 29, 14, 14, 14, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 14, 12, 2, 2, 2, 5, 5, 5, 5, 5, 12, 12] 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]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 481) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1nc2cc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)ccc2s1) `ZINC001183098967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183098967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001183098967 none CC(C)(C)OC(=O)Nc1nc2cc(NC(=O)[C@]([O-])([SiH3])Cc3c[nH]c4ccccc34)ccc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 28, 28, 14, 14, 14, 12, 12, 12, 12, 12, 2, 2, 1, 2, 1, 1, 1, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 12, 2, 2, 2, 5, 5, 5, 5, 5, 12, 12] 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]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183098967 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183098967 Building ZINC001183099055 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099055 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/482 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 22, 22, 22, 22, 22, 40, 43, 43, 42, 43, 43, 22, 22, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 22, 22, 22, 22, 40, 40, 43, 43, 43, 43, 43, 22, 22, 22, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/483 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/483' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 17, 17, 17, 30, 36, 36, 33, 36, 36, 17, 17, 4, 4, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 17, 17, 17, 17, 30, 30, 36, 36, 33, 36, 36, 17, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 484) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 22, 22, 22, 22, 22, 40, 43, 43, 42, 43, 43, 22, 22, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 22, 22, 22, 22, 40, 40, 43, 43, 43, 43, 43, 22, 22, 22, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 485) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 17, 17, 17, 30, 36, 36, 33, 36, 36, 17, 17, 4, 4, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 17, 17, 17, 17, 30, 30, 36, 36, 33, 36, 36, 17, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099055 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 Building ZINC001183099055 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099055 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 482) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 42, 44, 44, 42, 44, 44, 22, 22, 4, 4, 4, 4, 4, 4, 5, 5, 6, 6, 6, 6, 6, 22, 22, 22, 22, 42, 42, 44, 44, 43, 44, 44, 22, 22, 22, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 483) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 17, 17, 17, 31, 38, 38, 38, 38, 38, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 17, 17, 17, 17, 31, 31, 38, 38, 38, 38, 38, 17, 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, 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: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 484) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 22, 22, 22, 22, 22, 40, 43, 43, 42, 43, 43, 22, 22, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 22, 22, 22, 22, 40, 40, 43, 43, 43, 43, 43, 22, 22, 22, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 485) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 17, 17, 17, 30, 36, 36, 33, 36, 36, 17, 17, 4, 4, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 17, 17, 17, 17, 30, 30, 36, 36, 33, 36, 36, 17, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099055 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 Building ZINC001183099055 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099055 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 482) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 42, 44, 44, 42, 44, 44, 22, 22, 4, 4, 4, 4, 4, 4, 5, 5, 6, 6, 6, 6, 6, 22, 22, 22, 22, 42, 42, 44, 44, 43, 44, 44, 22, 22, 22, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 483) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 17, 17, 17, 31, 38, 38, 38, 38, 38, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 17, 17, 17, 17, 31, 31, 38, 38, 38, 38, 38, 17, 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, 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: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 484) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 22, 22, 22, 22, 22, 40, 43, 43, 42, 43, 43, 22, 22, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 22, 22, 22, 22, 40, 40, 43, 43, 43, 43, 43, 22, 22, 22, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 485) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 17, 17, 17, 30, 36, 36, 33, 36, 36, 17, 17, 4, 4, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 17, 17, 17, 17, 30, 30, 36, 36, 33, 36, 36, 17, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099055 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 Building ZINC001183099055 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099055 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 482) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/482: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 22, 22, 22, 22, 22, 42, 44, 44, 42, 44, 44, 22, 22, 4, 4, 4, 4, 4, 4, 5, 5, 6, 6, 6, 6, 6, 22, 22, 22, 22, 42, 42, 44, 44, 43, 44, 44, 22, 22, 22, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 483) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/483: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 17, 17, 17, 31, 38, 38, 38, 38, 38, 17, 17, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 17, 17, 17, 17, 31, 31, 38, 38, 38, 38, 38, 17, 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, 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: 158 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 484) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 22, 22, 22, 22, 22, 40, 43, 43, 42, 43, 43, 22, 22, 3, 3, 3, 3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 22, 22, 22, 22, 40, 40, 43, 43, 43, 43, 43, 22, 22, 22, 22] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 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: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 485) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1) `ZINC001183099055.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001183099055 none Nc1ccccc1N(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12)[C@H]1CC[N@@](Cc2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [4, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 1, 3, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 17, 17, 17, 17, 17, 30, 36, 36, 33, 36, 36, 17, 17, 4, 4, 4, 4, 4, 4, 5, 5, 7, 7, 7, 7, 7, 17, 17, 17, 17, 30, 30, 36, 36, 33, 36, 36, 17, 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, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099055 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099055 Building ZINC001183099124 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099124 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/486 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 30, 44, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/487 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/487' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 43, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 47, 47, 47, 47, 47, 47, 47, 47, 47, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 488) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 30, 44, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 489) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 43, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 47, 47, 47, 47, 47, 47, 47, 47, 47, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099124 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 Building ZINC001183099124 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099124 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 486) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 32, 47, 21, 21, 21, 21, 21, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 32, 21, 21, 21, 21, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 487) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 33, 47, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 33, 20, 20, 20, 20, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 488) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 30, 44, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 489) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 43, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 47, 47, 47, 47, 47, 47, 47, 47, 47, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099124 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 Building ZINC001183099124 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099124 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 486) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 32, 47, 21, 21, 21, 21, 21, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 32, 21, 21, 21, 21, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 487) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 33, 47, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 33, 20, 20, 20, 20, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 488) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 30, 44, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 489) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 43, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 47, 47, 47, 47, 47, 47, 47, 47, 47, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099124 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 Building ZINC001183099124 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001183099124 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 486) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 32, 47, 21, 21, 21, 21, 21, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 21, 21, 48, 48, 48, 48, 48, 48, 48, 48, 48, 32, 21, 21, 21, 21, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 21, 21, 21, 21] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 487) grep: /scratch/xiaobo/281161/xco-8058088.67/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: CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 47, 33, 47, 20, 20, 20, 20, 20, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 20, 20, 49, 49, 49, 49, 49, 49, 49, 49, 49, 33, 20, 20, 20, 20, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 20, 20, 20, 20] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 488) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 30, 44, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 48, 48, 48, 48, 48, 48, 48, 48, 48, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 489) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099124.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001183099124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 23 is the cov attach 4 23 0 4 23 1 4 23 2 3 23 2 26 to be deleted 27 to be deleted 28 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001183099124 none CC(C)(C)OC(=O)N[C@H]1CC[N@@](c2cccc(F)c2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 43, 18, 18, 18, 18, 18, 4, 4, 4, 3, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 18, 18, 47, 47, 47, 47, 47, 47, 47, 47, 47, 30, 18, 18, 18, 18, 4, 4, 4, 3, 2, 2, 3, 3, 3, 3, 3, 18, 18, 18, 18] 50 rigid atoms, others: [24, 25, 21, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099124 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099124 Building ZINC001183099181 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099181 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 490) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Oc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183099181 none CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 37, 26, 26, 26, 19, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 37, 37, 37, 37, 37, 37, 37, 37, 37, 26, 26, 26, 26, 26, 6, 6, 6, 3, 2, 2, 4, 4, 4, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 491) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Oc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183099181 none CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 28, 35, 28, 28, 28, 20, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 28, 28, 28, 28, 4, 4, 4, 3, 2, 2, 4, 4, 4, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099181 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 Building ZINC001183099181 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099181 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 490) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Oc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099181.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183099181 none CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 37, 26, 26, 26, 19, 6, 6, 6, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 26, 26, 37, 37, 37, 37, 37, 37, 37, 37, 37, 26, 26, 26, 26, 26, 6, 6, 6, 3, 2, 2, 4, 4, 4, 4, 4, 26, 26, 26, 26] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 491) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Oc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1) `ZINC001183099181.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183099181 none CC(C)(C)OC(=O)N1CCC(Oc2c(F)cccc2NC(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 12, 1, 1, 15, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 28, 35, 28, 28, 28, 20, 4, 4, 4, 4, 4, 4, 4, 3, 3, 1, 3, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 37, 37, 37, 37, 37, 37, 37, 37, 37, 28, 28, 28, 28, 28, 4, 4, 4, 3, 2, 2, 4, 4, 4, 4, 4, 28, 28, 28, 28] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099181 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099181 Building ZINC001183099291 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099291 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 492) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183099291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183099291 none CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)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.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.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 14, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 2, 13, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 13, 13, 13, 13, 13, 14, 14, 14, 14] 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]) total number of confs: 99 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 493) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183099291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183099291 none CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)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.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.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 12, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 2, 11, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 14, 14, 14, 14, 14, 12, 12, 12, 12] 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]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099291 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 Building ZINC001183099291 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099291 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 492) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183099291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183099291 none CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@@]([O-])([SiH3])Cc1c[nH]c3ccccc13)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.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.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 14, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 2, 13, 1, 1, 1, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 22, 22, 22, 22, 22, 22, 22, 22, 22, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 13, 13, 13, 13, 13, 14, 14, 14, 14] 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]) total number of confs: 99 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 493) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)CC2) `ZINC001183099291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001183099291 none CC(C)(C)OC(=O)N1Cc2ccccc2C12CCN(C(=O)[C@]([O-])([SiH3])Cc1c[nH]c3ccccc13)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.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.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 12, 17, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 2, 11, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 14, 14, 14, 14, 14, 12, 12, 12, 12] 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]) total number of confs: 89 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099291 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099291 Building ZINC001183099335 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099335 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 494) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183099335 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 6, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 1, 3, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 18, 14, 14, 14, 31, 31, 31, 31, 31, 3, 6, 6, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 495) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183099335 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 1, 3, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 18, 14, 14, 14, 33, 33, 33, 33, 33, 3, 7, 7, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099335 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 Building ZINC001183099335 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099335 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 494) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099335.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183099335 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 6, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 1, 3, 1, 1, 1, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 18, 14, 14, 14, 31, 31, 31, 31, 31, 3, 6, 6, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 495) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183099335.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001183099335 none COc1cccc(c2cc(=O)c3ccccc3o2)c1NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 14, 14, 14, 14, 14, 14, 14, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 3, 3, 1, 3, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 18, 18, 18, 14, 14, 14, 33, 33, 33, 33, 33, 3, 7, 7, 13, 13, 13, 13, 13] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099335 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099335 Building ZINC001183099556 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099556 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 496) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1N) `ZINC001183099556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001183099556 none CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 12, 10, 12, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 21, 21, 21, 21, 21, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 497) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1N) `ZINC001183099556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001183099556 none CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 14, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099556 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 Building ZINC001183099556 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183099556 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 496) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1N) `ZINC001183099556.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183099556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001183099556 none CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 12, 10, 12, 2, 2, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 21, 21, 21, 21, 21, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 2, 2, 2] 50 rigid atoms, others: [9, 10, 11, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 497) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1N) `ZINC001183099556.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183099556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001183099556 none CCOC(=O)Nc1ccc(N(Cc2ccc(F)cc2)C(=O)[C@]([O-])([SiH3])Cc2c[nH]c3ccccc23)cc1N NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 14, 4, 4, 4, 4, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 23, 23, 23, 23, 23, 12, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/281161/xco-8058088.67/working/building/ZINC001183099556 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183099556 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183099556 Building ZINC001183100259 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100259 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 498) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100259 none O=C(N[C@@]1(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 27, 9, 9, 9, 9, 9, 9, 26, 13, 13, 13, 13, 13, 13, 7, 7, 15, 15, 15, 15, 15] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 120 number of broken/clashed sets: 268 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 499) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100259 none O=C(N[C@@]1(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 27, 9, 9, 9, 9, 9, 9, 30, 15, 15, 15, 15, 15, 15, 6, 6, 14, 14, 14, 14, 14] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 125 number of broken/clashed sets: 267 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100259 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 Building ZINC001183100259 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100259 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 498) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100259 none O=C(N[C@@]1(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 27, 9, 9, 9, 9, 9, 9, 26, 13, 13, 13, 13, 13, 13, 7, 7, 15, 15, 15, 15, 15] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 120 number of broken/clashed sets: 268 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 499) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100259 none O=C(N[C@@]1(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 6, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 27, 9, 9, 9, 9, 9, 9, 30, 15, 15, 15, 15, 15, 15, 6, 6, 14, 14, 14, 14, 14] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 125 number of broken/clashed sets: 267 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100259 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100259 Building ZINC001183100260 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100260 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 500) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100260 none O=C(N[C@@]1(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 27, 9, 9, 9, 9, 9, 9, 30, 15, 15, 15, 15, 15, 15, 7, 7, 14, 14, 14, 14, 14] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 126 number of broken/clashed sets: 288 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 501) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100260 none O=C(N[C@@]1(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 27, 9, 9, 9, 9, 9, 9, 26, 13, 13, 13, 13, 13, 13, 6, 6, 11, 11, 11, 11, 11] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 112 number of broken/clashed sets: 294 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100260 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 Building ZINC001183100260 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100260 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 500) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100260 none O=C(N[C@@]1(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 27, 9, 9, 9, 9, 9, 9, 30, 15, 15, 15, 15, 15, 15, 7, 7, 14, 14, 14, 14, 14] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 126 number of broken/clashed sets: 288 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 501) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100260 none O=C(N[C@@]1(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 27, 9, 9, 9, 9, 9, 9, 26, 13, 13, 13, 13, 13, 13, 6, 6, 11, 11, 11, 11, 11] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 112 number of broken/clashed sets: 294 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100260 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100260 Building ZINC001183100261 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100261 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 502) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100261 none O=C(N[C@]1(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 33, 11, 11, 11, 11, 11, 11, 32, 16, 16, 16, 16, 16, 16, 7, 7, 17, 17, 17, 17, 17] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 142 number of broken/clashed sets: 285 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 503) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100261 none O=C(N[C@]1(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 33, 11, 11, 11, 11, 11, 11, 28, 14, 14, 14, 14, 14, 14, 8, 8, 20, 20, 20, 20, 20] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 139 number of broken/clashed sets: 265 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100261 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 Building ZINC001183100261 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100261 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 502) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100261 none O=C(N[C@]1(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [4, 1, 4, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 4, 33, 11, 11, 11, 11, 11, 11, 32, 16, 16, 16, 16, 16, 16, 7, 7, 17, 17, 17, 17, 17] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 142 number of broken/clashed sets: 285 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 503) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100261 none O=C(N[C@]1(O)C=Cc2ccccc2[C@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 8, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 33, 11, 11, 11, 11, 11, 11, 28, 14, 14, 14, 14, 14, 14, 8, 8, 20, 20, 20, 20, 20] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 139 number of broken/clashed sets: 265 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100261 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100261 Building ZINC001183100262 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100262 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 504) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100262 none O=C(N[C@]1(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 27, 9, 9, 9, 9, 9, 9, 24, 12, 12, 12, 12, 12, 12, 9, 9, 21, 21, 21, 21, 21] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 129 number of broken/clashed sets: 294 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 505) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100262 none O=C(N[C@]1(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 36, 12, 12, 12, 12, 12, 12, 32, 16, 16, 16, 16, 16, 16, 9, 9, 19, 19, 19, 19, 19] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 153 number of broken/clashed sets: 288 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100262 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 Building ZINC001183100262 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100262 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 504) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100262 none O=C(N[C@]1(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 27, 9, 9, 9, 9, 9, 9, 24, 12, 12, 12, 12, 12, 12, 9, 9, 21, 21, 21, 21, 21] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 129 number of broken/clashed sets: 294 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 505) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC001183100262 none O=C(N[C@]1(O)C=Cc2ccccc2[C@@H]1c1c(O)ccc2ccccc21)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 2 hydrogens need rotated 300 conformations in input total number of sets (complete confs): 300 using faster count positions algorithm for large data unique positions, atoms: [5, 1, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 36, 12, 12, 12, 12, 12, 12, 32, 16, 16, 16, 16, 16, 16, 9, 9, 19, 19, 19, 19, 19] 300 rigid atoms, others: [1, 26, 27, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 153 number of broken/clashed sets: 288 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100262 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100262 Building ZINC001183100266 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100266 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 506) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183100266 none O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 12, 12, 12, 12, 21, 21, 21, 21, 32, 32, 34, 34, 32, 34, 34, 21, 21, 12, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 12, 21, 21, 32, 32, 34, 34, 32, 34, 34, 21, 21, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 36, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 507) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183100266 none O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 12, 12, 12, 12, 22, 22, 18, 18, 33, 33, 35, 35, 33, 35, 35, 22, 22, 12, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 12, 22, 22, 33, 33, 35, 35, 33, 35, 35, 22, 22, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 36, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100266 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 Building ZINC001183100266 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100266 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 506) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183100266 none O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 12, 12, 12, 12, 21, 21, 21, 21, 32, 32, 34, 34, 32, 34, 34, 21, 21, 12, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 12, 21, 21, 32, 32, 34, 34, 32, 34, 34, 21, 21, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 36, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 507) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001183100266 none O=C(NCc1coc(c2ccc(OCc3ccccc3)cc2)n1)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 12, 12, 12, 12, 22, 22, 18, 18, 33, 33, 35, 35, 33, 35, 35, 22, 22, 12, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 7, 7, 12, 22, 22, 33, 33, 35, 35, 33, 35, 35, 22, 22, 2, 2, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 36, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100266 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100266 Building ZINC001183100546 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100546 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 508) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183100546 none O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 22, 11, 11, 2, 3, 3, 6, 6, 6, 6, 6] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 127 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 509) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183100546 none O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 12, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100546 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 Building ZINC001183100546 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183100546 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 508) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100546.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183100546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183100546 none O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 5, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 2, 5, 5, 11, 11, 11, 11, 11, 11, 11, 2, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 25, 25, 25, 25, 25, 25, 25, 11, 11, 11, 11, 22, 11, 11, 2, 3, 3, 6, 6, 6, 6, 6] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 127 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 509) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12) `ZINC001183100546.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183100546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 26 is the cov attach 4 26 0 4 26 1 4 26 2 3 26 2 29 to be deleted 30 to be deleted 31 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001183100546 none O=C(Nc1ccc2ccccc2c1)[C@H](Cc1ccc(O)cc1)NC(=O)[C@]([O-])([SiH3])Cc1c[nH]c2ccccc12 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 12, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 8, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [6, 4, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 2, 4, 4, 6, 6, 6, 6, 6, 6, 6, 2, 1, 2, 1, 1, 1, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6, 12, 6, 6, 2, 2, 2, 4, 4, 4, 4, 4] 100 rigid atoms, others: [24, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183100546 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183100546 Building ZINC001183356470 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183356470 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 510) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(C3=Nc4ccccc4Oc4ccc(Cl)cc43)CC2)cc1) `ZINC001183356470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183356470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183356470 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3=Nc4ccccc4Oc4ccc(Cl)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 2, 4, 5, 12, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 13, 13, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 511) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(C3=Nc4ccccc4Oc4ccc(Cl)cc43)CC2)cc1) `ZINC001183356470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183356470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183356470 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3=Nc4ccccc4Oc4ccc(Cl)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 5, 10, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183356470 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 Building ZINC001183356470 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183356470 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 510) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(C3=Nc4ccccc4Oc4ccc(Cl)cc43)CC2)cc1) `ZINC001183356470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183356470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183356470 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCN(C3=Nc4ccccc4Oc4ccc(Cl)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 2, 4, 5, 12, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 13, 13, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 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]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 511) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(C3=Nc4ccccc4Oc4ccc(Cl)cc43)CC2)cc1) `ZINC001183356470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183356470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183356470 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCN(C3=Nc4ccccc4Oc4ccc(Cl)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 4, 5, 10, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 11, 11, 2, 2, 2, 2, 2, 2, 2, 11, 11, 11, 11, 50, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 2, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183356470 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183356470 Building ZINC001183358109 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358109 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 512) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CN(C(=O)OC(C)(C)C)c4ccc(Cl)cc43)CC2)cc1) `ZINC001183358109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183358109 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CN(C(=O)OC(C)(C)C)c4ccc(Cl)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 10, 18, 18, 18, 18, 18, 18, 32, 32, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 513) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CN(C(=O)OC(C)(C)C)c4ccc(Cl)cc43)CC2)cc1) `ZINC001183358109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183358109 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CN(C(=O)OC(C)(C)C)c4ccc(Cl)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 10, 16, 16, 16, 16, 16, 16, 28, 28, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358109 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 Building ZINC001183358109 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358109 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 512) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CN(C(=O)OC(C)(C)C)c4ccc(Cl)cc43)CC2)cc1) `ZINC001183358109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183358109 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC3(CN(C(=O)OC(C)(C)C)c4ccc(Cl)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 10, 18, 18, 18, 18, 18, 18, 32, 32, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 2, 2, 2, 2, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 18, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 513) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CN(C(=O)OC(C)(C)C)c4ccc(Cl)cc43)CC2)cc1) `ZINC001183358109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183358109 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC3(CN(C(=O)OC(C)(C)C)c4ccc(Cl)cc43)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 16, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 4, 10, 16, 16, 16, 16, 16, 16, 28, 28, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 16, 16, 2, 2, 2, 2, 2, 2, 2, 16, 16, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 16, 16, 16, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358109 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358109 Building ZINC001183358213 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358213 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 514) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3[nH]nc(c4ccc(Oc5ccccc5)cc4)c32)cc1) `ZINC001183358213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358213 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3[nH]nc(c4ccc(Oc5ccccc5)cc4)c32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 6, 10, 42, 50, 50, 42, 50, 50, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 15, 15, 50, 50, 42, 50, 50, 15, 15, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 515) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3[nH]nc(c4ccc(Oc5ccccc5)cc4)c32)cc1) `ZINC001183358213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358213 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3[nH]nc(c4ccc(Oc5ccccc5)cc4)c32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 11, 14, 44, 50, 50, 44, 50, 50, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 14, 14, 50, 50, 44, 50, 50, 14, 14, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358213 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 Building ZINC001183358213 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358213 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 514) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3[nH]nc(c4ccc(Oc5ccccc5)cc4)c32)cc1) `ZINC001183358213.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358213 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ncnc3[nH]nc(c4ccc(Oc5ccccc5)cc4)c32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 6, 10, 42, 50, 50, 42, 50, 50, 15, 15, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 15, 15, 50, 50, 42, 50, 50, 15, 15, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 515) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3[nH]nc(c4ccc(Oc5ccccc5)cc4)c32)cc1) `ZINC001183358213.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358213 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ncnc3[nH]nc(c4ccc(Oc5ccccc5)cc4)c32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 8, 1, 8, 1, 8, 6, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 11, 14, 44, 50, 50, 44, 50, 50, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 2, 6, 14, 14, 50, 50, 44, 50, 50, 14, 14, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358213 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358213 Building ZINC001183358221 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358221 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 516) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)cc3)c(Br)n2)c1) `ZINC001183358221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001183358221 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)cc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 24, 36, 24, 24, 24, 24, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 3, 3, 3, 24, 50, 50, 50, 50, 50, 24, 24, 24, 3, 3, 2, 2, 2, 4, 4, 4, 2, 2, 24] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 517) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)cc3)c(Br)n2)c1) `ZINC001183358221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001183358221 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)cc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 25, 37, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 3, 3, 3, 25, 50, 50, 50, 50, 50, 25, 25, 25, 3, 3, 2, 2, 2, 4, 4, 4, 2, 2, 25] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358221 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 Building ZINC001183358221 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358221 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 516) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)cc3)c(Br)n2)c1) `ZINC001183358221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001183358221 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccc(OC)cc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 24, 36, 24, 24, 24, 24, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 3, 3, 3, 24, 50, 50, 50, 50, 50, 24, 24, 24, 3, 3, 2, 2, 2, 4, 4, 4, 2, 2, 24] 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]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 517) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)cc3)c(Br)n2)c1) `ZINC001183358221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001183358221 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccc(OC)cc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 25, 37, 25, 25, 25, 25, 3, 3, 3, 3, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 1, 4, 2, 2, 3, 3, 3, 25, 50, 50, 50, 50, 50, 25, 25, 25, 3, 3, 2, 2, 2, 4, 4, 4, 2, 2, 25] 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]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358221 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358221 Building ZINC001183358694 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358694 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 518) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(O[C@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1) `ZINC001183358694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358694 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(O[C@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 19, 43, 43, 46, 46, 43, 43, 46, 46, 43, 47, 47, 47, 47, 47, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 46, 46, 46, 46, 47, 47, 47, 47, 5, 5, 5, 5, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 519) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(O[C@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1) `ZINC001183358694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358694 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(O[C@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 16, 39, 39, 44, 44, 39, 39, 44, 44, 39, 45, 45, 45, 45, 45, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 44, 44, 44, 44, 45, 45, 45, 45, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358694 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 Building ZINC001183358694 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358694 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 518) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(O[C@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1) `ZINC001183358694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358694 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(O[C@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 19, 43, 43, 46, 46, 43, 43, 46, 46, 43, 47, 47, 47, 47, 47, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 46, 46, 46, 46, 47, 47, 47, 47, 5, 5, 5, 5, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 160 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 519) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(O[C@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1) `ZINC001183358694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358694 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(O[C@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 16, 39, 39, 44, 44, 39, 39, 44, 44, 39, 45, 45, 45, 45, 45, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 44, 44, 44, 44, 45, 45, 45, 45, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358694 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358694 Building ZINC001183358695 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358695 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 520) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(O[C@@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1) `ZINC001183358695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(O[C@@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 18, 44, 44, 46, 46, 44, 44, 46, 46, 44, 48, 48, 48, 48, 48, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 46, 46, 46, 46, 48, 48, 48, 48, 5, 5, 5, 5, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 521) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(O[C@@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1) `ZINC001183358695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(O[C@@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 17, 41, 41, 46, 46, 46, 46, 46, 46, 41, 47, 47, 47, 47, 47, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 46, 46, 46, 46, 47, 47, 47, 47, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358695 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 Building ZINC001183358695 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183358695 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 520) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(O[C@@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1) `ZINC001183358695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183358695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358695 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(O[C@@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 18, 44, 44, 46, 46, 44, 44, 46, 46, 44, 48, 48, 48, 48, 48, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 46, 46, 46, 46, 48, 48, 48, 48, 5, 5, 5, 5, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 521) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(O[C@@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1) `ZINC001183358695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183358695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183358695 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(O[C@@H](c3ccc(Cl)cc3)c3ccccn3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 12, 5, 7, 1, 1, 1, 1, 16, 1, 1, 1, 1, 1, 1, 1, 8, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 17, 41, 41, 46, 46, 46, 46, 46, 46, 41, 47, 47, 47, 47, 47, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 46, 46, 46, 46, 47, 47, 47, 47, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183358695 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183358695 Building ZINC001183364331 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183364331 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 522) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(c2cccc(Br)c2)c2ncnc3ccc(N)cc32)cc1) `ZINC001183364331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183364331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001183364331 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(c2cccc(Br)c2)c2ncnc3ccc(N)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 5, 5, 12, 37, 37, 24, 37, 37, 37, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 37, 37, 35, 37, 18, 18, 18, 18, 18, 18, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 523) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(c2cccc(Br)c2)c2ncnc3ccc(N)cc32)cc1) `ZINC001183364331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183364331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001183364331 none COc1ccc([C@]([O-])([SiH3])C(=O)N(c2cccc(Br)c2)c2ncnc3ccc(N)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 12, 37, 37, 24, 37, 37, 37, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 37, 37, 36, 37, 18, 18, 18, 18, 18, 18, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183364331 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 Building ZINC001183364331 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183364331 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 522) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(c2cccc(Br)c2)c2ncnc3ccc(N)cc32)cc1) `ZINC001183364331.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183364331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001183364331 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(c2cccc(Br)c2)c2ncnc3ccc(N)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 4, 4, 1, 1, 1, 1, 5, 5, 12, 37, 37, 24, 37, 37, 37, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 37, 37, 35, 37, 18, 18, 18, 18, 18, 18, 4, 4] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 523) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(c2cccc(Br)c2)c2ncnc3ccc(N)cc32)cc1) `ZINC001183364331.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183364331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001183364331 none COc1ccc([C@]([O-])([SiH3])C(=O)N(c2cccc(Br)c2)c2ncnc3ccc(N)cc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 17, 1, 1, 8, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 5, 5, 12, 37, 37, 24, 37, 37, 37, 12, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 4, 4, 4, 4, 4, 4, 4, 37, 37, 36, 37, 18, 18, 18, 18, 18, 18, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183364331 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364331 Building ZINC001183364770 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183364770 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 524) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3cccc(Cl)c3C)ccc2OC)cc1) `ZINC001183364770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183364770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183364770 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3cccc(Cl)c3C)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 11, 11, 11, 30, 30, 27, 30, 30, 30, 30, 6, 6, 6, 6, 11, 5, 5, 5, 5, 5, 5, 5, 3, 6, 11, 30, 30, 30, 30, 30, 30, 6, 6, 11, 11, 11, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 525) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3cccc(Cl)c3C)ccc2OC)cc1) `ZINC001183364770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183364770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183364770 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3cccc(Cl)c3C)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 11, 5, 5, 5, 5, 5, 5, 5, 3, 6, 11, 30, 30, 30, 30, 30, 30, 6, 6, 11, 11, 11, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183364770 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 Building ZINC001183364770 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183364770 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 524) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3cccc(Cl)c3C)ccc2OC)cc1) `ZINC001183364770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183364770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183364770 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3cccc(Cl)c3C)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 11, 11, 11, 30, 30, 27, 30, 30, 30, 30, 6, 6, 6, 6, 11, 5, 5, 5, 5, 5, 5, 5, 3, 6, 11, 30, 30, 30, 30, 30, 30, 6, 6, 11, 11, 11, 5, 5] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 525) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3cccc(Cl)c3C)ccc2OC)cc1) `ZINC001183364770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183364770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183364770 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2cc(C(=O)Nc3cccc(Cl)c3C)ccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 5, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 11, 11, 11, 30, 30, 30, 30, 30, 30, 30, 6, 6, 6, 6, 11, 5, 5, 5, 5, 5, 5, 5, 3, 6, 11, 30, 30, 30, 30, 30, 30, 6, 6, 11, 11, 11, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183364770 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183364770 Building ZINC001183365100 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183365100 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 526) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(CCc2cc(OC)c(Cl)cc2OC)Cc2ccccc2OC)cc1) `ZINC001183365100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183365100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183365100 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCc2cc(OC)c(Cl)cc2OC)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 17, 17, 17, 32, 17, 17, 17, 17, 17, 29, 2, 4, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 32, 32, 32, 17, 29, 29, 29, 4, 4, 5, 5, 5, 5, 9, 9, 9, 2, 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, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 527) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(CCc2cc(OC)c(Cl)cc2OC)Cc2ccccc2OC)cc1) `ZINC001183365100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183365100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183365100 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CCc2cc(OC)c(Cl)cc2OC)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 17, 17, 17, 32, 17, 17, 17, 17, 17, 29, 2, 4, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 32, 32, 32, 17, 29, 29, 29, 4, 4, 5, 5, 5, 5, 9, 9, 9, 2, 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, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183365100 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 Building ZINC001183365100 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183365100 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 526) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(CCc2cc(OC)c(Cl)cc2OC)Cc2ccccc2OC)cc1) `ZINC001183365100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183365100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183365100 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(CCc2cc(OC)c(Cl)cc2OC)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 17, 17, 17, 32, 17, 17, 17, 17, 17, 29, 2, 4, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 32, 32, 32, 17, 29, 29, 29, 4, 4, 5, 5, 5, 5, 9, 9, 9, 2, 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, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 527) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(CCc2cc(OC)c(Cl)cc2OC)Cc2ccccc2OC)cc1) `ZINC001183365100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183365100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001183365100 none COc1ccc([C@]([O-])([SiH3])C(=O)N(CCc2cc(OC)c(Cl)cc2OC)Cc2ccccc2OC)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 16, 1, 1, 12, 5, 5, 1, 1, 1, 1, 1, 1, 12, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 17, 17, 17, 32, 17, 17, 17, 17, 17, 29, 2, 4, 5, 5, 5, 5, 5, 5, 9, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 17, 32, 32, 32, 17, 29, 29, 29, 4, 4, 5, 5, 5, 5, 9, 9, 9, 2, 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, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183365100 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365100 Building ZINC001183365174 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183365174 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 528) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(Oc3ccnc4cc(OC)c(OC)cc43)cc2)cc1) `ZINC001183365174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183365174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183365174 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 20, 22, 22, 22, 22, 22, 22, 22, 42, 22, 22, 50, 22, 22, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 22, 22, 22, 42, 42, 42, 50, 50, 50, 22, 4, 4, 3, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 529) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(Oc3ccnc4cc(OC)c(OC)cc43)cc2)cc1) `ZINC001183365174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183365174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183365174 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 22, 22, 22, 22, 22, 22, 22, 42, 22, 22, 50, 22, 22, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 22, 22, 22, 42, 42, 42, 50, 50, 50, 22, 4, 4, 3, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183365174 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 Building ZINC001183365174 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183365174 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 528) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(Oc3ccnc4cc(OC)c(OC)cc43)cc2)cc1) `ZINC001183365174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183365174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183365174 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 2, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 20, 22, 22, 22, 22, 22, 22, 22, 42, 22, 22, 50, 22, 22, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 22, 22, 22, 42, 42, 42, 50, 50, 50, 22, 4, 4, 3, 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 529) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(Oc3ccnc4cc(OC)c(OC)cc43)cc2)cc1) `ZINC001183365174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183365174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183365174 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 20, 22, 22, 22, 22, 22, 22, 22, 42, 22, 22, 50, 22, 22, 4, 4, 3, 3, 3, 3, 3, 3, 3, 2, 4, 4, 22, 22, 22, 42, 42, 42, 50, 50, 50, 22, 4, 4, 3, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183365174 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365174 Building ZINC001183365533 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183365533 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 530) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(c3cc4cc(OC)cc(Br)c4o3)CC2)cc1) `ZINC001183365533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183365533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001183365533 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3cc4cc(OC)cc(Br)c4o3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 17, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 5, 6, 6, 6, 6, 30, 30, 30, 30, 30, 50, 30, 30, 30, 30, 30, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 30, 30, 50, 50, 50, 30, 6, 6, 6, 6, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 531) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(c3cc4cc(OC)cc(Br)c4o3)CC2)cc1) `ZINC001183365533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183365533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001183365533 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3cc4cc(OC)cc(Br)c4o3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 17, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 28, 28, 28, 28, 28, 50, 28, 28, 28, 28, 28, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 28, 28, 50, 50, 50, 28, 5, 5, 5, 5, 2, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183365533 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 Building ZINC001183365533 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183365533 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 530) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(c3cc4cc(OC)cc(Br)c4o3)CC2)cc1) `ZINC001183365533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183365533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001183365533 none COc1ccc([C@@]([O-])([SiH3])C(=O)N2CCC(c3cc4cc(OC)cc(Br)c4o3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 17, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 5, 6, 6, 6, 6, 30, 30, 30, 30, 30, 50, 30, 30, 30, 30, 30, 6, 6, 2, 2, 2, 2, 2, 2, 2, 6, 6, 6, 6, 6, 30, 30, 50, 50, 50, 30, 6, 6, 6, 6, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 531) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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(c3cc4cc(OC)cc(Br)c4o3)CC2)cc1) `ZINC001183365533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183365533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001183365533 none COc1ccc([C@]([O-])([SiH3])C(=O)N2CCC(c3cc4cc(OC)cc(Br)c4o3)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 1, 1, 17, 1, 12, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 1, 1, 2, 3, 4, 5, 5, 5, 5, 28, 28, 28, 28, 28, 50, 28, 28, 28, 28, 28, 5, 5, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 28, 28, 50, 50, 50, 28, 5, 5, 5, 5, 2, 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]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183365533 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183365533 Building ZINC001183348501 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183348501 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 532) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c3ccccc3oc2C(=O)c2ccc(OC)c(OC)c2)cc1) `ZINC001183348501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183348501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183348501 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c3ccccc3oc2C(=O)c2ccc(OC)c(OC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 24, 24, 24, 24, 44, 24, 24, 47, 24, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 8, 24, 24, 44, 44, 44, 47, 47, 47, 24, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 533) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c3ccccc3oc2C(=O)c2ccc(OC)c(OC)c2)cc1) `ZINC001183348501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183348501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183348501 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c3ccccc3oc2C(=O)c2ccc(OC)c(OC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 24, 24, 24, 24, 44, 24, 24, 47, 24, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 8, 24, 24, 44, 44, 44, 47, 47, 47, 24, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183348501 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 Building ZINC001183348501 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183348501 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 532) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c3ccccc3oc2C(=O)c2ccc(OC)c(OC)c2)cc1) `ZINC001183348501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183348501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183348501 none COc1ccc([C@@]([O-])([SiH3])C(=O)Nc2c3ccccc3oc2C(=O)c2ccc(OC)c(OC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 24, 24, 24, 24, 44, 24, 24, 47, 24, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 8, 24, 24, 44, 44, 44, 47, 47, 47, 24, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 533) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c3ccccc3oc2C(=O)c2ccc(OC)c(OC)c2)cc1) `ZINC001183348501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183348501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001183348501 none COc1ccc([C@]([O-])([SiH3])C(=O)Nc2c3ccccc3oc2C(=O)c2ccc(OC)c(OC)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 9, 9, 24, 24, 24, 24, 44, 24, 24, 47, 24, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 8, 24, 24, 44, 44, 44, 47, 47, 47, 24, 4, 4] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183348501 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183348501 Building ZINC001183366898 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183366898 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 534) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(C)cc(F)c2)C2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC001183366898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183366898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001183366898 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(C)cc(F)c2)C2CCN(C(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 3, 4, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 4, 4, 15, 15, 30, 32, 32, 32, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 106 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 535) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(C)cc(F)c2)C2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC001183366898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183366898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001183366898 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(C)cc(F)c2)C2CCN(C(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 8, 8, 8, 8, 8, 8, 8, 3, 4, 4, 4, 4, 17, 17, 31, 31, 31, 31, 4, 4, 2, 2, 2, 2, 2, 2, 2, 5, 5, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 86 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183366898 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 Building ZINC001183366898 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183366898 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 534) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(C)cc(F)c2)C2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC001183366898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183366898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001183366898 none COc1ccc([C@]([O-])([SiH3])C(=O)N(Cc2cc(C)cc(F)c2)C2CCN(C(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 2, 2, 1, 1, 1, 1, 2, 2, 3, 4, 9, 9, 9, 9, 9, 9, 9, 2, 4, 4, 4, 4, 15, 15, 30, 32, 32, 32, 4, 4, 2, 2, 2, 2, 2, 2, 2, 4, 4, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 106 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 535) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(C)cc(F)c2)C2CCN(C(=O)OC(C)(C)C)CC2)cc1) `ZINC001183366898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183366898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 71 natoms 70 natoms 69 natoms 68 names: ZINC001183366898 none COc1ccc([C@@]([O-])([SiH3])C(=O)N(Cc2cc(C)cc(F)c2)C2CCN(C(=O)OC(C)(C)C)CC2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'F', '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', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 1, 15, 1, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 8, 8, 8, 8, 8, 8, 8, 3, 4, 4, 4, 4, 17, 17, 31, 31, 31, 31, 4, 4, 2, 2, 2, 2, 2, 2, 2, 5, 5, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 4, 2, 2] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67]) total number of confs: 86 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183366898 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183366898 Building ZINC001183376497 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183376497 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 536) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1) `ZINC001183376497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183376497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183376497 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 1, 1, 1, 1, 4, 4, 12, 20, 20, 20, 20, 20, 38, 38, 47, 47, 47, 47, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 20, 20, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 537) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1) `ZINC001183376497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183376497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183376497 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 12, 17, 17, 17, 17, 17, 35, 35, 47, 47, 47, 47, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 17, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 17, 17, 17, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183376497 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 Building ZINC001183376497 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183376497 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 536) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1) `ZINC001183376497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183376497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183376497 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 1, 1, 1, 1, 4, 4, 12, 20, 20, 20, 20, 20, 38, 38, 47, 47, 47, 47, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 6, 6, 6, 4, 20, 20, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 20, 20, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 537) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1) `ZINC001183376497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183376497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183376497 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 4, 12, 17, 17, 17, 17, 17, 35, 35, 47, 47, 47, 47, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 4, 17, 17, 17, 17, 47, 47, 47, 47, 47, 47, 47, 47, 47, 17, 17, 17, 6, 6] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/281161/xco-8058088.67/working/building/ZINC001183376497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183376497 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376497 Building ZINC001183376498 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183376498 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 538) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1) `ZINC001183376498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183376498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183376498 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 9, 19, 19, 19, 19, 19, 39, 39, 47, 47, 47, 47, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 19, 19, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 539) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1) `ZINC001183376498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183376498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183376498 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 4, 4, 10, 22, 22, 22, 22, 22, 38, 38, 48, 48, 48, 48, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 5, 5, 5, 5, 4, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 22, 22, 22, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183376498 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 Building ZINC001183376498 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183376498 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 538) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1) `ZINC001183376498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183376498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183376498 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 1, 6, 6, 1, 1, 1, 1, 3, 3, 9, 19, 19, 19, 19, 19, 39, 39, 47, 47, 47, 47, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 6, 6, 6, 3, 19, 19, 19, 19, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 19, 19, 6, 6] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 539) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1) `ZINC001183376498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183376498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183376498 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H]2CCN(C(=O)OC(C)(C)C)c3cc(Br)ccc32)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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', '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, 8, 1, 11, 12, 5, 5, 5, 5, 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, 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 5, 5, 1, 1, 1, 1, 4, 4, 10, 22, 22, 22, 22, 22, 38, 38, 48, 48, 48, 48, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 5, 5, 5, 5, 4, 22, 22, 22, 22, 48, 48, 48, 48, 48, 48, 48, 48, 48, 22, 22, 22, 5, 5] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183376498 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183376498 Building ZINC001183377042 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377042 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 540) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc3cccc(Cl)c3c(=O)n2c2ccccc2)cc1) `ZINC001183377042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183377042 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc3cccc(Cl)c3c(=O)n2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 26, 41, 41, 41, 39, 41, 41, 41, 41, 41, 41, 41, 42, 42, 42, 42, 42, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 12, 41, 26, 41, 41, 42, 42, 42, 42, 42, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 541) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc3cccc(Cl)c3c(=O)n2c2ccccc2)cc1) `ZINC001183377042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183377042 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc3cccc(Cl)c3c(=O)n2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 1, 8, 8, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 40, 40, 40, 40, 40, 8, 8, 8, 8, 8, 8, 8, 6, 12, 12, 12, 39, 27, 39, 39, 40, 40, 40, 40, 40, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183377042 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 Building ZINC001183377042 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377042 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 540) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc3cccc(Cl)c3c(=O)n2c2ccccc2)cc1) `ZINC001183377042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183377042 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc3cccc(Cl)c3c(=O)n2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 9, 9, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 26, 41, 41, 41, 39, 41, 41, 41, 41, 41, 41, 41, 42, 42, 42, 42, 42, 9, 9, 9, 9, 9, 9, 9, 6, 12, 12, 12, 41, 26, 41, 41, 42, 42, 42, 42, 42, 9, 9] 50 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 541) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc3cccc(Cl)c3c(=O)n2c2ccccc2)cc1) `ZINC001183377042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183377042 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@@H](C)c2cc3cccc(Cl)c3c(=O)n2c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 1, 8, 8, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 27, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 40, 40, 40, 40, 40, 8, 8, 8, 8, 8, 8, 8, 6, 12, 12, 12, 39, 27, 39, 39, 40, 40, 40, 40, 40, 8, 8] 50 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 161 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183377042 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377042 Building ZINC001183377408 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377408 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 542) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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](c2ccccc2)C(O)(c2ccccc2)c2ccccc2)cc1) `ZINC001183377408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183377408 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)C(O)(c2ccccc2)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 8, 8, 8, 10, 10, 12, 12, 10, 12, 12, 10, 25, 25, 36, 36, 25, 36, 36, 25, 39, 39, 26, 39, 39, 9, 9, 9, 9, 9, 9, 9, 8, 12, 12, 10, 12, 12, 75, 36, 36, 25, 36, 36, 39, 39, 30, 39, 39, 9, 9] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 313 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 543) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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](c2ccccc2)C(O)(c2ccccc2)c2ccccc2)cc1) `ZINC001183377408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183377408 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)C(O)(c2ccccc2)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 1, 9, 9, 1, 1, 1, 1, 8, 8, 8, 11, 11, 14, 14, 11, 14, 14, 11, 29, 29, 37, 37, 29, 37, 37, 29, 39, 39, 29, 39, 39, 9, 9, 9, 9, 9, 9, 9, 8, 14, 14, 11, 14, 14, 87, 37, 37, 29, 37, 37, 39, 39, 33, 39, 39, 9, 9] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 325 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183377408 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 Building ZINC001183377408 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001183377408 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 542) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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](c2ccccc2)C(O)(c2ccccc2)c2ccccc2)cc1) `ZINC001183377408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001183377408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183377408 none COc1ccc([C@@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)C(O)(c2ccccc2)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 1, 1, 9, 9, 1, 1, 1, 1, 8, 8, 8, 10, 10, 12, 12, 10, 12, 12, 10, 25, 25, 36, 36, 25, 36, 36, 25, 39, 39, 26, 39, 39, 9, 9, 9, 9, 9, 9, 9, 8, 12, 12, 10, 12, 12, 75, 36, 36, 25, 36, 36, 39, 39, 30, 39, 39, 9, 9] 150 rigid atoms, others: [5, 6, 7, 8] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 313 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 543) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=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](c2ccccc2)C(O)(c2ccccc2)c2ccccc2)cc1) `ZINC001183377408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001183377408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001183377408 none COc1ccc([C@]([O-])([SiH3])C(=O)N[C@H](c2ccccc2)C(O)(c2ccccc2)c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 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, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [9, 2, 1, 9, 9, 1, 1, 1, 1, 8, 8, 8, 11, 11, 14, 14, 11, 14, 14, 11, 29, 29, 37, 37, 29, 37, 37, 29, 39, 39, 29, 39, 39, 9, 9, 9, 9, 9, 9, 9, 8, 14, 14, 11, 14, 14, 87, 37, 37, 29, 37, 37, 39, 39, 33, 39, 39, 9, 9] 150 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 325 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001183377408 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001183377408 Building ZINC001184250805 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184250805 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 544) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H](C)Cc1cccc(C(F)(F)F)c1) `ZINC001184250805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184250805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184250805 none CCCCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H](C)Cc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 6, 5, 3, 1, 3, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 14, 8, 5, 5, 5, 5, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 6, 6, 6, 6, 4, 4, 8, 8, 16, 14, 14, 14, 8, 5, 5, 5, 7, 7, 12, 12, 12, 12] 100 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, 54, 55, 56, 57, 58, 59]) total number of confs: 96 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 545) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H](C)Cc1cccc(C(F)(F)F)c1) `ZINC001184250805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184250805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184250805 none CCCCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H](C)Cc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 8, 4, 2, 1, 2, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 15, 10, 4, 4, 4, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 8, 8, 8, 8, 6, 6, 10, 10, 20, 15, 15, 15, 10, 4, 4, 4, 7, 7, 13, 13, 13, 13] 100 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, 54, 55, 56, 57, 58, 59]) total number of confs: 124 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184250805 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 Building ZINC001184250805 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184250805 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 544) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H](C)Cc1cccc(C(F)(F)F)c1) `ZINC001184250805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184250805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184250805 none CCCCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H](C)Cc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [7, 6, 6, 5, 3, 1, 3, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 14, 8, 5, 5, 5, 5, 7, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 6, 6, 6, 6, 4, 4, 8, 8, 16, 14, 14, 14, 8, 5, 5, 5, 7, 7, 12, 12, 12, 12] 100 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, 54, 55, 56, 57, 58, 59]) total number of confs: 96 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 545) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H](C)Cc1cccc(C(F)(F)F)c1) `ZINC001184250805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184250805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184250805 none CCCCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@@H](C)Cc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 8, 4, 2, 1, 2, 1, 1, 1, 6, 10, 10, 10, 10, 10, 10, 15, 10, 4, 4, 4, 4, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 9, 9, 8, 8, 8, 8, 6, 6, 10, 10, 20, 15, 15, 15, 10, 4, 4, 4, 7, 7, 13, 13, 13, 13] 100 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, 54, 55, 56, 57, 58, 59]) total number of confs: 124 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184250805 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250805 Building ZINC001184250806 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184250806 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 546) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H](C)Cc1cccc(C(F)(F)F)c1) `ZINC001184250806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184250806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184250806 none CCCCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H](C)Cc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 8, 4, 2, 1, 2, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 14, 8, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9, 8, 8, 8, 8, 5, 5, 8, 8, 16, 14, 14, 14, 8, 4, 4, 4, 7, 7, 14, 14, 14, 14] 100 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, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 547) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H](C)Cc1cccc(C(F)(F)F)c1) `ZINC001184250806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184250806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184250806 none CCCCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H](C)Cc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 6, 5, 3, 1, 3, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 11, 8, 5, 5, 5, 5, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 6, 6, 6, 6, 4, 4, 8, 8, 16, 11, 11, 11, 8, 5, 5, 5, 8, 8, 15, 15, 15, 15] 100 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, 54, 55, 56, 57, 58, 59]) total number of confs: 104 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184250806 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 Building ZINC001184250806 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184250806 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 546) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H](C)Cc1cccc(C(F)(F)F)c1) `ZINC001184250806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184250806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184250806 none CCCCN(C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H](C)Cc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [9, 8, 8, 4, 2, 1, 2, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 14, 8, 4, 4, 4, 4, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 9, 9, 8, 8, 8, 8, 5, 5, 8, 8, 16, 14, 14, 14, 8, 4, 4, 4, 7, 7, 14, 14, 14, 14] 100 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, 54, 55, 56, 57, 58, 59]) total number of confs: 119 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 547) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H](C)Cc1cccc(C(F)(F)F)c1) `ZINC001184250806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184250806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 63 natoms 62 natoms 61 natoms 60 names: ZINC001184250806 none CCCCN(C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1)[C@H](C)Cc1cccc(C(F)(F)F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 5, 7, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [8, 6, 6, 5, 3, 1, 3, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 11, 8, 5, 5, 5, 5, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 8, 6, 6, 6, 6, 4, 4, 8, 8, 16, 11, 11, 11, 8, 5, 5, 5, 8, 8, 15, 15, 15, 15] 100 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, 54, 55, 56, 57, 58, 59]) total number of confs: 104 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184250806 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184250806 Building ZINC001184252276 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252276 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 548) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Oc1cc(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c(C(C)(C)C)cc1C(C)(C)C) `ZINC001184252276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001184252276 none COC(=O)Oc1cc(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c(C(C)(C)C)cc1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 16, 27, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 8, 3, 3, 3, 6, 6, 12, 12, 12, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 102 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 549) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Oc1cc(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c(C(C)(C)C)cc1C(C)(C)C) `ZINC001184252276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001184252276 none COC(=O)Oc1cc(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c(C(C)(C)C)cc1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 16, 30, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 7, 3, 3, 3, 6, 6, 12, 12, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 111 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184252276 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 Building ZINC001184252276 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252276 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 548) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Oc1cc(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c(C(C)(C)C)cc1C(C)(C)C) `ZINC001184252276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001184252276 none COC(=O)Oc1cc(NC(=O)[C@@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c(C(C)(C)C)cc1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 16, 27, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 8, 3, 3, 3, 6, 6, 12, 12, 12, 12, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 102 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 549) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Oc1cc(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c(C(C)(C)C)cc1C(C)(C)C) `ZINC001184252276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 70 natoms 69 natoms 68 natoms 67 names: ZINC001184252276 none COC(=O)Oc1cc(NC(=O)[C@]([O-])([SiH3])Cc2ccc(O)c(OC)c2)c(C(C)(C)C)cc1C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 12, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 3, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 16, 30, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 30, 30, 30, 7, 3, 3, 3, 6, 6, 12, 12, 12, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 100 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 111 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184252276 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252276 Building ZINC001184252754 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252754 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 550) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)ccc1O) `ZINC001184252754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252754 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 14, 16, 16, 16, 16, 16, 16, 16, 28, 16, 16, 28, 16, 16, 3, 3, 3, 3, 3, 3, 4, 4, 4, 3, 2, 2, 1, 3, 3, 16, 16, 16, 28, 28, 28, 28, 28, 28, 16, 3, 3, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 551) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)ccc1O) `ZINC001184252754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252754 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 14, 16, 16, 16, 16, 16, 16, 16, 28, 16, 16, 28, 16, 16, 3, 3, 3, 3, 3, 3, 4, 4, 4, 3, 2, 2, 1, 3, 3, 16, 16, 16, 28, 28, 28, 28, 28, 28, 16, 3, 3, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184252754 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 Building ZINC001184252754 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252754 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 550) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)ccc1O) `ZINC001184252754.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252754 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 14, 16, 16, 16, 16, 16, 16, 16, 28, 16, 16, 28, 16, 16, 3, 3, 3, 3, 3, 3, 4, 4, 4, 3, 2, 2, 1, 3, 3, 16, 16, 16, 28, 28, 28, 28, 28, 28, 16, 3, 3, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 551) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)ccc1O) `ZINC001184252754.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184252754 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccc(Oc3ccnc4cc(OC)c(OC)cc43)cc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 2, 14, 16, 16, 16, 16, 16, 16, 16, 28, 16, 16, 28, 16, 16, 3, 3, 3, 3, 3, 3, 4, 4, 4, 3, 2, 2, 1, 3, 3, 16, 16, 16, 28, 28, 28, 28, 28, 28, 16, 3, 3, 3, 3, 6] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 42] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184252754 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252754 Building ZINC001184252810 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252810 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 552) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOc1c(Cl)cc(Cl)cc1Cl)C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184252810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252810 none CCCN(CCOc1c(Cl)cc(Cl)cc1Cl)C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 3, 2, 3, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 23, 23, 3, 3, 6, 6, 12, 14, 14, 14, 6] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 553) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOc1c(Cl)cc(Cl)cc1Cl)C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184252810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252810 none CCCN(CCOc1c(Cl)cc(Cl)cc1Cl)C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 3, 3, 3, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 17, 9, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 16, 16, 5, 5, 9, 9, 18, 17, 17, 17, 9] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184252810 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 Building ZINC001184252810 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184252810 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 552) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOc1c(Cl)cc(Cl)cc1Cl)C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184252810.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184252810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252810 none CCCN(CCOc1c(Cl)cc(Cl)cc1Cl)C(=O)[C@@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 3, 2, 3, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 2, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 6, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 23, 23, 3, 3, 6, 6, 12, 14, 14, 14, 6] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 553) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCOc1c(Cl)cc(Cl)cc1Cl)C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1) `ZINC001184252810.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184252810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184252810 none CCCN(CCOc1c(Cl)cc(Cl)cc1Cl)C(=O)[C@]([O-])([SiH3])Cc1ccc(O)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 5, 12, 1, 1, 16, 1, 1, 16, 1, 1, 16, 1, 11, 5, 12, 5, 1, 1, 1, 1, 12, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 4, 3, 3, 3, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 3, 1, 1, 1, 5, 9, 9, 9, 9, 9, 9, 17, 9, 5, 5, 5, 5, 5, 4, 4, 7, 7, 7, 7, 16, 16, 5, 5, 9, 9, 18, 17, 17, 17, 9] 100 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 106 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184252810 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184252810 Building ZINC001184253020 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253020 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 554) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c2cc(C(F)(F)F)cc(C(F)(F)F)c2)ccc1O) `ZINC001184253020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184253020 none COc1cc(C[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c2cc(C(F)(F)F)cc(C(F)(F)F)c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 8, 8, 4, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 10, 10, 10, 10, 10, 10, 3, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 10, 10, 10, 8, 4, 4, 2, 2, 2, 3, 3, 3, 10, 3, 10, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 555) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c2cc(C(F)(F)F)cc(C(F)(F)F)c2)ccc1O) `ZINC001184253020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184253020 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c2cc(C(F)(F)F)cc(C(F)(F)F)c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 12, 12, 6, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 12, 12, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 6, 6, 3, 3, 3, 4, 4, 4, 12, 4, 12, 12, 12, 24] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253020 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 Building ZINC001184253020 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253020 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 554) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c2cc(C(F)(F)F)cc(C(F)(F)F)c2)ccc1O) `ZINC001184253020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184253020 none COc1cc(C[C@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c2cc(C(F)(F)F)cc(C(F)(F)F)c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [10, 8, 8, 8, 4, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 10, 10, 10, 10, 10, 10, 3, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 10, 10, 10, 8, 4, 4, 2, 2, 2, 3, 3, 3, 10, 3, 10, 8, 8, 16] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 74 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 555) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c2cc(C(F)(F)F)cc(C(F)(F)F)c2)ccc1O) `ZINC001184253020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 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: ZINC001184253020 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N(C)[C@@H](C)c2cc(C(F)(F)F)cc(C(F)(F)F)c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 15, 15, 15, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 12, 12, 12, 6, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 12, 12, 12, 12, 12, 12, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 12, 6, 6, 3, 3, 3, 4, 4, 4, 12, 4, 12, 12, 12, 24] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 97 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253020 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253020 Building ZINC001184253337 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253337 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 556) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@@H]2OCc2ccccc2)ccc1O) `ZINC001184253337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253337 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 7, 7, 6, 7, 7, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 7, 7, 6, 7, 7, 4, 4, 8] 42 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 49 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 557) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@@H]2OCc2ccccc2)ccc1O) `ZINC001184253337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253337 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 6, 6, 4, 6, 6, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 4, 4, 8] 28 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 48 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253337 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 Building ZINC001184253337 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253337 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 556) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@@H]2OCc2ccccc2)ccc1O) `ZINC001184253337.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253337 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [6, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 7, 7, 6, 7, 7, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 7, 7, 6, 7, 7, 4, 4, 8] 42 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 49 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 557) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@@H]2OCc2ccccc2)ccc1O) `ZINC001184253337.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253337 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 4, 6, 6, 4, 6, 6, 4, 4, 4, 4, 8, 8, 8, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 6, 4, 6, 6, 4, 4, 8] 28 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 48 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253337 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253337 Building ZINC001184253339 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253339 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 558) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@@H]2OCc2ccccc2)ccc1O) `ZINC001184253339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253339 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [11, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 10, 12, 12, 10, 12, 12, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 12, 12, 10, 12, 12, 4, 4, 8] 46 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 78 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 559) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@@H]2OCc2ccccc2)ccc1O) `ZINC001184253339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253339 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 7, 7, 6, 7, 7, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 4, 4, 8] 36 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 55 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253339 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 Building ZINC001184253339 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253339 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 558) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@@H]2OCc2ccccc2)ccc1O) `ZINC001184253339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253339 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [11, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 10, 12, 12, 10, 12, 12, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 10, 10, 12, 12, 10, 12, 12, 4, 4, 8] 46 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 78 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 559) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@@H]2OCc2ccccc2)ccc1O) `ZINC001184253339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253339 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [11, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 7, 7, 6, 7, 7, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 7, 6, 7, 7, 4, 4, 8] 36 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 55 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253339 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253339 Building ZINC001184253341 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253341 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 560) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@H]2OCc2ccccc2)ccc1O) `ZINC001184253341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253341 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 4, 4, 8] 18 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 36 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 561) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@H]2OCc2ccccc2)ccc1O) `ZINC001184253341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253341 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8] 10 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 23 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253341 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 Building ZINC001184253341 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253341 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 560) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@H]2OCc2ccccc2)ccc1O) `ZINC001184253341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253341 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 5, 5, 4, 4, 4, 4, 6, 6, 6, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 4, 4, 8] 18 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 36 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 561) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@H]2OCc2ccccc2)ccc1O) `ZINC001184253341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253341 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@H]2CC[C@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8] 10 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 23 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253341 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253341 Building ZINC001184253342 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253342 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 562) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@H]2OCc2ccccc2)ccc1O) `ZINC001184253342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253342 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 20, 31, 31, 26, 31, 31, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 20, 20, 31, 31, 31, 31, 31, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 563) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@H]2OCc2ccccc2)ccc1O) `ZINC001184253342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253342 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 23, 23, 19, 23, 23, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 23, 23, 23, 23, 23, 4, 4, 8] 80 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 105 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253342 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 Building ZINC001184253342 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253342 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 562) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@H]2OCc2ccccc2)ccc1O) `ZINC001184253342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253342 none COc1cc(C[C@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 8, 20, 31, 31, 26, 31, 31, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 20, 20, 31, 31, 31, 31, 31, 4, 4, 8] 100 rigid atoms, others: [5, 6, 7, 8, 9, 10] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 150 number of broken/clashed sets: 100 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 563) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@H]2OCc2ccccc2)ccc1O) `ZINC001184253342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184253342 none COc1cc(C[C@@]([O-])([SiH3])C(=O)N([C@H](C)c2ccccc2)[C@@H]2CC[C@H]2OCc2ccccc2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [11, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 12, 23, 23, 19, 23, 23, 4, 4, 4, 4, 11, 11, 11, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 23, 23, 23, 23, 23, 4, 4, 8] 80 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55] set([0, 1, 2, 3, 4, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 105 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253342 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253342 Building ZINC001184253605 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253605 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 564) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Oc2ccc3ccccc3c2)ccc1O) `ZINC001184253605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184253605 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Oc2ccc3ccccc3c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 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: [10, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 2, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 565) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Oc2ccc3ccccc3c2)ccc1O) `ZINC001184253605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184253605 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Oc2ccc3ccccc3c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 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: [10, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 2, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253605 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 Building ZINC001184253605 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184253605 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 564) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Oc2ccc3ccccc3c2)ccc1O) `ZINC001184253605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184253605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184253605 none COc1cc(C[C@@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Oc2ccc3ccccc3c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 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: [10, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 2, 3, 3, 3, 3, 30, 30, 30, 30, 30, 30, 30, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 565) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Oc2ccc3ccccc3c2)ccc1O) `ZINC001184253605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184253605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184253605 none COc1cc(C[C@]([O-])([SiH3])C(=O)Nc2ccccc2C(=O)Oc2ccc3ccccc3c2)ccc1O NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 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, 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: [10, 5, 5, 5, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 9, 9, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 5, 5, 5, 5, 10, 10, 10, 5, 3, 3, 2, 3, 3, 3, 3, 29, 29, 29, 29, 29, 29, 29, 5, 5, 10] 100 rigid atoms, others: [8, 5, 6, 7] set([0, 1, 2, 3, 4, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184253605 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184253605 Building ZINC001184318880 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318880 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 566) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184318880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318880 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 13, 30, 50, 50, 50, 50, 50, 50, 50, 50, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4, 4, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 567) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184318880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318880 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 7, 2, 8, 3, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318880 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 Building ZINC001184318880 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318880 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 566) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184318880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318880 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 13, 30, 50, 50, 50, 50, 50, 50, 50, 50, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4, 4, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 567) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184318880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318880 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 7, 2, 8, 3, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318880 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318880 Building ZINC001184318881 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318881 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 568) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184318881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318881 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 13, 30, 50, 50, 50, 50, 50, 50, 50, 50, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4, 4, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 569) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184318881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318881 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 7, 2, 8, 3, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318881 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 Building ZINC001184318881 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318881 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 568) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184318881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318881 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 2, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 13, 30, 50, 50, 50, 50, 50, 50, 50, 50, 4, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 4, 4, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 3, 3, 3, 3] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 569) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184318881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184318881 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 23, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 7, 2, 8, 3, 4, 6, 5] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 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: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318881 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318881 Building ZINC001184316691 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184316691 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 570) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1) `ZINC001184316691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184316691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184316691 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 4, 4, 4, 10, 10, 10, 12, 6, 6, 15, 10, 10, 13, 10, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 16, 16, 16, 32, 16, 4, 10, 12, 12, 12, 15, 15, 15, 13, 13, 13, 10] 100 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 571) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1) `ZINC001184316691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184316691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184316691 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 10, 10, 10, 15, 6, 6, 18, 10, 10, 15, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 21, 21, 21, 42, 21, 6, 10, 15, 15, 15, 19, 18, 18, 15, 15, 15, 10] 100 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184316691 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 Building ZINC001184316691 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184316691 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 570) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1) `ZINC001184316691.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184316691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184316691 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 4, 4, 4, 10, 10, 10, 12, 6, 6, 15, 10, 10, 13, 10, 3, 3, 3, 3, 3, 3, 3, 3, 2, 4, 16, 16, 16, 32, 16, 4, 10, 12, 12, 12, 15, 15, 15, 13, 13, 13, 10] 100 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 571) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1) `ZINC001184316691.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184316691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184316691 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 21, 21, 21, 21, 21, 21, 6, 6, 6, 10, 10, 10, 15, 6, 6, 18, 10, 10, 15, 10, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 21, 21, 21, 42, 21, 6, 10, 15, 15, 15, 19, 18, 18, 15, 15, 15, 10] 100 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]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184316691 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316691 Building ZINC001184316693 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184316693 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 572) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1) `ZINC001184316693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184316693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184316693 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 5, 5, 5, 11, 11, 11, 16, 5, 6, 18, 11, 11, 14, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 18, 18, 18, 36, 18, 5, 11, 16, 16, 16, 18, 18, 18, 14, 14, 14, 11] 100 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 573) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1) `ZINC001184316693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184316693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184316693 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 5, 5, 5, 11, 11, 11, 15, 6, 6, 20, 11, 11, 16, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 16, 16, 16, 32, 16, 5, 11, 15, 15, 15, 20, 20, 20, 16, 16, 16, 11] 100 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184316693 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 Building ZINC001184316693 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184316693 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 572) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1) `ZINC001184316693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184316693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184316693 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 5, 5, 5, 11, 11, 11, 16, 5, 6, 18, 11, 11, 14, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 18, 18, 18, 36, 18, 5, 11, 16, 16, 16, 18, 18, 18, 14, 14, 14, 11] 100 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]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 573) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1) `ZINC001184316693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184316693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001184316693 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(c2cccc(O)c2)cc1c1cc(OC)c(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', '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', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 12, 5, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 5, 5, 5, 11, 11, 11, 15, 6, 6, 20, 11, 11, 16, 11, 2, 2, 2, 2, 2, 2, 2, 2, 3, 5, 16, 16, 16, 32, 16, 5, 11, 15, 15, 15, 20, 20, 20, 16, 16, 16, 11] 100 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]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184316693 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184316693 Building ZINC001184317420 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317420 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 574) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184317420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184317420 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 41, 41, 50, 50, 50, 50, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 575) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184317420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184317420 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 42, 42, 50, 50, 50, 50, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184317420 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 Building ZINC001184317420 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317420 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 574) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184317420.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184317420 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 41, 41, 50, 50, 50, 50, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 575) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184317420.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184317420 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 42, 42, 50, 50, 50, 50, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184317420 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317420 Building ZINC001184317422 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317422 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 576) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184317422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184317422 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 577) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184317422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184317422 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 44, 44, 50, 50, 50, 50, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184317422 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 Building ZINC001184317422 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184317422 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 576) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184317422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184317422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184317422 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 40, 40, 50, 50, 50, 50, 19, 19, 19, 2, 2, 2, 2, 2, 2, 2, 2, 3, 6, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 577) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184317422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184317422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184317422 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 44, 44, 50, 50, 50, 50, 22, 22, 22, 2, 2, 2, 2, 2, 2, 2, 2, 3, 7, 22, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 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]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184317422 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184317422 Building ZINC001184318042 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318042 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 578) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318042 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 3, 7, 6, 7, 7, 7, 10, 11, 16, 21, 21, 16, 21, 21, 7, 7, 7, 7, 7, 7, 7, 15, 15, 36, 37, 37, 37, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 168 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 579) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318042 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 10, 11, 11, 11, 11, 12, 15, 20, 22, 22, 20, 22, 22, 11, 11, 11, 11, 11, 11, 11, 24, 24, 38, 40, 40, 40, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 20, 20, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318042 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 Building ZINC001184318042 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318042 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 578) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318042.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318042 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 3, 7, 6, 7, 7, 7, 10, 11, 16, 21, 21, 16, 21, 21, 7, 7, 7, 7, 7, 7, 7, 15, 15, 36, 37, 37, 37, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 168 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 579) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318042.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318042 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 10, 11, 11, 11, 11, 12, 15, 20, 22, 22, 20, 22, 22, 11, 11, 11, 11, 11, 11, 11, 24, 24, 38, 40, 40, 40, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 20, 20, 22, 22, 22, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 40, 40, 40, 40, 40, 40, 40, 40, 40, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318042 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318042 Building ZINC001184318043 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318043 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 580) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318043 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 9, 9, 9, 9, 9, 11, 12, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 15, 15, 23, 23, 23, 23, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 581) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318043 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 2, 6, 6, 6, 6, 6, 10, 14, 23, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 14, 14, 28, 29, 29, 29, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 23, 23, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 169 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318043 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 Building ZINC001184318043 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318043 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 580) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318043.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318043 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 2, 9, 9, 9, 9, 9, 11, 12, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 15, 15, 23, 23, 23, 23, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 106 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 581) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318043.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318043 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 2, 6, 6, 6, 6, 6, 10, 14, 23, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 14, 14, 28, 29, 29, 29, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 23, 23, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 169 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318043 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318043 Building ZINC001184318044 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318044 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 582) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318044 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 3, 7, 6, 7, 7, 7, 10, 11, 16, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 17, 17, 37, 38, 38, 38, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 150 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 583) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318044 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 11, 12, 12, 12, 12, 13, 16, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 23, 23, 38, 39, 39, 39, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 12] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318044 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 Building ZINC001184318044 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318044 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 582) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318044.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318044 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 3, 7, 6, 7, 7, 7, 10, 11, 16, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 17, 17, 37, 38, 38, 38, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 16, 16, 21, 21, 21, 21, 21, 7, 7, 7, 7, 7, 7, 7, 7, 38, 38, 38, 38, 38, 38, 38, 38, 38, 7, 7, 7, 7] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 150 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 583) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318044.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318044 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 11, 12, 12, 12, 12, 13, 16, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 23, 23, 38, 39, 39, 39, 12, 12, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 19, 19, 19, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 39, 39, 39, 39, 39, 39, 39, 39, 39, 12, 12, 12, 12] 50 rigid atoms, others: [2, 5, 6] set([0, 1, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 132 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318044 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318044 Building ZINC001184318045 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318045 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 584) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318045 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 8, 9, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 9, 9, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 585) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318045 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 5, 5, 8, 12, 23, 26, 26, 23, 26, 26, 5, 5, 5, 5, 5, 5, 5, 12, 12, 30, 32, 32, 32, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 23, 23, 26, 26, 23, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 177 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318045 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 Building ZINC001184318045 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184318045 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 584) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184318045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318045 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 5, 5, 5, 5, 8, 9, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 9, 9, 17, 17, 17, 17, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 8, 8, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 585) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184318045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184318045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184318045 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 5, 5, 5, 5, 5, 8, 12, 23, 26, 26, 23, 26, 26, 5, 5, 5, 5, 5, 5, 5, 12, 12, 30, 32, 32, 32, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 23, 23, 26, 26, 23, 26, 26, 5, 5, 5, 5, 5, 5, 5, 5, 32, 32, 32, 32, 32, 32, 32, 32, 32, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 177 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184318045 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184318045 Building ZINC001184320767 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184320767 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 586) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1) `ZINC001184320767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184320767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184320767 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 3, 3, 13, 33, 37, 37, 37, 33, 45, 45, 45, 45, 45, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 13, 13, 37, 37, 37, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 6, 10, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 587) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1) `ZINC001184320767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184320767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184320767 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 3, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 14, 34, 37, 37, 37, 34, 47, 47, 47, 47, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 14, 14, 37, 37, 37, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 6, 10, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184320767 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 Building ZINC001184320767 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184320767 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 586) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1) `ZINC001184320767.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184320767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184320767 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 3, 3, 13, 33, 37, 37, 37, 33, 45, 45, 45, 45, 45, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 13, 13, 37, 37, 37, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 6, 10, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 587) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1) `ZINC001184320767.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184320767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184320767 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 3, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 14, 34, 37, 37, 37, 34, 47, 47, 47, 47, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 14, 14, 37, 37, 37, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 6, 10, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184320767 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184320767 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320767 Building ZINC001184320772 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184320772 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 588) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1) `ZINC001184320772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184320772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184320772 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 3, 4, 4, 4, 4, 4, 4, 6, 6, 4, 6, 14, 34, 37, 37, 37, 34, 47, 47, 47, 47, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 14, 14, 37, 37, 37, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 6, 10, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 589) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1) `ZINC001184320772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184320772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184320772 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 33, 37, 37, 37, 33, 45, 45, 45, 45, 45, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 13, 13, 37, 37, 37, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 6, 10, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184320772 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 Building ZINC001184320772 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184320772 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 588) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1) `ZINC001184320772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184320772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184320772 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 4, 4, 3, 4, 4, 4, 4, 4, 4, 6, 6, 4, 6, 14, 34, 37, 37, 37, 34, 47, 47, 47, 47, 47, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 6, 14, 14, 37, 37, 37, 47, 47, 47, 47, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 6, 10, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 589) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1) `ZINC001184320772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184320772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184320772 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)c1ccc(CN(C(=O)OC)c2cccnc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 1, 1, 1, 1, 8, 1, 1, 1, 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] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total 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, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 13, 33, 37, 37, 37, 33, 45, 45, 45, 45, 45, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 5, 5, 13, 13, 37, 37, 37, 45, 45, 45, 45, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 8, 9, 7, 6, 10, 5] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184320772 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184320772 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184320772 Building ZINC001184323185 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323185 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 590) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184323185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184323185 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 6, 12, 12, 6, 8, 29, 30, 30, 30, 45, 45, 30, 30, 29, 30, 30, 29, 30, 30, 12, 12, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 30, 45, 45, 30, 30, 30, 30, 30, 30, 12, 12, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 591) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184323185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184323185 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 8, 15, 15, 13, 13, 33, 33, 33, 33, 50, 50, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 33, 50, 50, 33, 33, 33, 33, 33, 33, 15, 15, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184323185 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 Building ZINC001184323185 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323185 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 590) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184323185.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184323185 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 5, 6, 12, 12, 6, 8, 29, 30, 30, 30, 45, 45, 30, 30, 29, 30, 30, 29, 30, 30, 12, 12, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 30, 45, 45, 30, 30, 30, 30, 30, 30, 12, 12, 6, 6, 6, 6, 6, 6] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 591) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184323185.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184323185 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 5, 8, 15, 15, 13, 13, 33, 33, 33, 33, 50, 50, 33, 33, 33, 33, 33, 33, 33, 33, 15, 15, 8, 8, 8, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 33, 50, 50, 33, 33, 33, 33, 33, 33, 15, 15, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184323185 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323185 Building ZINC001184323186 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323186 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 592) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184323186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184323186 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 6, 7, 12, 12, 12, 12, 28, 28, 28, 28, 45, 45, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 28, 45, 45, 28, 28, 28, 28, 28, 28, 12, 12, 7, 7, 7, 7, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 593) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184323186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184323186 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 5, 7, 11, 11, 9, 7, 28, 30, 30, 30, 50, 50, 30, 28, 30, 30, 30, 28, 30, 30, 11, 11, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 30, 50, 50, 30, 30, 30, 28, 30, 30, 11, 11, 7, 7, 7, 7, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184323186 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 Building ZINC001184323186 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184323186 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 592) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184323186.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184323186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184323186 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 2, 1, 1, 1, 3, 3, 6, 7, 12, 12, 12, 12, 28, 28, 28, 28, 45, 45, 28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 3, 12, 12, 28, 45, 45, 28, 28, 28, 28, 28, 28, 12, 12, 7, 7, 7, 7, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 593) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184323186.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184323186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184323186 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 5, 7, 11, 11, 9, 7, 28, 30, 30, 30, 50, 50, 30, 28, 30, 30, 30, 28, 30, 30, 11, 11, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 30, 50, 50, 30, 30, 30, 28, 30, 30, 11, 11, 7, 7, 7, 7, 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, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184323186 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184323186 Building ZINC001184324170 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324170 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 594) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1) `ZINC001184324170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184324170 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 8, 8, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 6, 6, 14, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 43, 43, 43, 43, 43, 43, 46, 46, 27, 6, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 17, 17, 27, 27, 27, 27, 27, 27, 43, 43, 43, 46, 46, 46, 46, 46, 46, 46, 27, 27, 9, 9, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 595) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1) `ZINC001184324170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184324170 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 8, 8, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 6, 6, 17, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 41, 41, 41, 41, 41, 41, 44, 44, 29, 6, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 19, 19, 29, 29, 29, 29, 29, 29, 41, 41, 41, 44, 44, 44, 44, 44, 44, 44, 29, 29, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]) total number of confs: 164 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184324170 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 Building ZINC001184324170 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324170 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 594) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1) `ZINC001184324170.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184324170 none CC[C@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 8, 8, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 6, 6, 14, 17, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 43, 43, 43, 43, 43, 43, 46, 46, 27, 6, 9, 9, 9, 9, 9, 3, 3, 3, 3, 3, 3, 3, 3, 3, 14, 14, 17, 17, 27, 27, 27, 27, 27, 27, 43, 43, 43, 46, 46, 46, 46, 46, 46, 46, 27, 27, 9, 9, 9, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]) total number of confs: 162 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 595) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1) `ZINC001184324170.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184324170 none CC[C@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 8, 8, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 6, 6, 17, 19, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 41, 41, 41, 41, 41, 41, 44, 44, 29, 6, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 19, 19, 29, 29, 29, 29, 29, 29, 41, 41, 41, 44, 44, 44, 44, 44, 44, 44, 29, 29, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]) total number of confs: 164 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184324170 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324170 Building ZINC001184324171 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324171 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 596) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1) `ZINC001184324171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184324171 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 8, 8, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 6, 6, 14, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 46, 46, 29, 6, 9, 9, 6, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 17, 17, 29, 29, 29, 29, 29, 29, 44, 44, 44, 46, 46, 46, 46, 46, 46, 46, 29, 29, 9, 9, 6, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]) total number of confs: 170 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 597) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1) `ZINC001184324171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184324171 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 8, 8, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 6, 6, 17, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 42, 42, 42, 42, 42, 42, 46, 46, 30, 6, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 18, 18, 30, 30, 30, 30, 30, 30, 42, 42, 42, 46, 46, 46, 46, 46, 46, 46, 30, 30, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]) total number of confs: 167 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184324171 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 Building ZINC001184324171 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324171 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 596) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1) `ZINC001184324171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184324171 none CC[C@@H](C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 8, 8, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 1, 4, 4, 1, 1, 1, 3, 3, 3, 6, 6, 14, 17, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 44, 44, 44, 44, 44, 44, 46, 46, 29, 6, 9, 9, 6, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 3, 14, 14, 17, 17, 29, 29, 29, 29, 29, 29, 44, 44, 44, 46, 46, 46, 46, 46, 46, 46, 29, 29, 9, 9, 6, 9, 9] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]) total number of confs: 170 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 597) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1) `ZINC001184324171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184324171 none CC[C@@H](C)[C@]([O-])([SiH3])C(=O)N[C@@H](CCN1[C@@H]2CC[C@H]1C[C@H](n1c(C)nnc1C(C)C)C2)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'C.2', 'C.3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 10, 5, 7, 5, 5, 5, 7, 5, 5, 7, 8, 1, 5, 8, 8, 1, 5, 5, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 3, 3, 3, 6, 6, 17, 18, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 42, 42, 42, 42, 42, 42, 46, 46, 30, 6, 11, 11, 11, 11, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 17, 17, 18, 18, 30, 30, 30, 30, 30, 30, 42, 42, 42, 46, 46, 46, 46, 46, 46, 46, 30, 30, 11, 11, 11, 11, 11] 50 rigid atoms, others: [2, 5, 6, 7] set([0, 1, 3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75]) total number of confs: 167 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184324171 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324171 Building ZINC001184324268 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324268 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 598) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])CC(C)C)cc(OC)c1OC) `ZINC001184324268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184324268 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])CC(C)C)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 9, 9, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 13, 3, 3, 14, 13, 13, 13, 9, 3, 9, 9, 9, 18, 9, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 13, 13, 13, 14, 14, 14] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 599) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc(OC)c1OC) `ZINC001184324268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184324268 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 9, 9, 9, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 13, 3, 4, 14, 11, 11, 11, 9, 3, 9, 9, 9, 18, 9, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 13, 13, 13, 14, 14, 14] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184324268 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 Building ZINC001184324268 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324268 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 598) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])CC(C)C)cc(OC)c1OC) `ZINC001184324268.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184324268 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])CC(C)C)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [13, 9, 9, 9, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 13, 3, 3, 14, 13, 13, 13, 9, 3, 9, 9, 9, 18, 9, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 13, 13, 13, 14, 14, 14] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 90 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 599) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc(OC)c1OC) `ZINC001184324268.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184324268 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 9, 9, 9, 3, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 1, 3, 1, 1, 1, 2, 2, 2, 9, 9, 9, 13, 3, 4, 14, 11, 11, 11, 9, 3, 9, 9, 9, 18, 9, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 9, 13, 13, 13, 14, 14, 14] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184324268 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324268 Building ZINC001184324275 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324275 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 600) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184324275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184324275 none CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 40, 40, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17] 50 rigid atoms, others: [0, 1, 2, 3, 36, 33, 38, 32, 8, 9, 7, 34, 35, 39, 4, 6, 5, 37, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 601) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184324275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184324275 none CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 44, 44, 50, 50, 50, 50, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14] 50 rigid atoms, others: [0, 1, 2, 3, 36, 33, 38, 32, 8, 9, 7, 34, 35, 39, 4, 6, 5, 37, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184324275 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 Building ZINC001184324275 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184324275 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 600) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184324275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184324275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184324275 none CC(C)C[C@@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 17, 17, 17, 17, 40, 40, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 17, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17] 50 rigid atoms, others: [0, 1, 2, 3, 36, 33, 38, 32, 8, 9, 7, 34, 35, 39, 4, 6, 5, 37, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 601) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1) `ZINC001184324275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184324275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184324275 none CC(C)C[C@]([O-])([SiH3])C(=O)Nc1ncc(Br)nc1c1ccc(C(=O)OC(C)(C)C)c(F)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 1, 8, 1, 1, 17, 8, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 14, 14, 14, 14, 44, 44, 50, 50, 50, 50, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 14, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14] 50 rigid atoms, others: [0, 1, 2, 3, 36, 33, 38, 32, 8, 9, 7, 34, 35, 39, 4, 6, 5, 37, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184324275 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184324275 Building ZINC001184328007 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184328007 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 602) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184328007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184328007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184328007 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 3, 14, 16, 17, 17, 17, 21, 25, 26, 27, 27, 26, 27, 27, 17, 17, 17, 17, 17, 17, 17, 29, 29, 39, 39, 39, 39, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 26, 26, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 17, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 146 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 603) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184328007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184328007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184328007 none CC(C)C[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 3, 11, 11, 12, 12, 12, 16, 22, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 12, 21, 21, 27, 27, 27, 27, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 12] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184328007 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 Building ZINC001184328007 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184328007 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 602) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184328007.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184328007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184328007 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 3, 14, 16, 17, 17, 17, 21, 25, 26, 27, 27, 26, 27, 27, 17, 17, 17, 17, 17, 17, 17, 29, 29, 39, 39, 39, 39, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 2, 21, 21, 26, 26, 27, 27, 27, 27, 27, 17, 17, 17, 17, 17, 17, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 39, 17, 17, 17, 17] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 146 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 603) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184328007.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184328007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184328007 none CC(C)C[C@]([O-])([SiH3])C(=O)N1[C@@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 1, 1, 1, 3, 11, 11, 12, 12, 12, 16, 22, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 12, 21, 21, 27, 27, 27, 27, 12, 12, 2, 2, 2, 2, 2, 2, 2, 2, 2, 16, 16, 29, 29, 29, 29, 29, 29, 29, 12, 12, 12, 12, 12, 12, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 12, 12] 50 rigid atoms, others: [3, 4, 5] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184328007 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328007 Building ZINC001184328009 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184328009 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 604) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184328009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184328009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184328009 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 15, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 15, 15, 24, 24, 24, 24, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 605) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184328009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184328009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184328009 none CC(C)C[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 10, 16, 24, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 15, 15, 26, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 24, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184328009 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 Building ZINC001184328009 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184328009 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 604) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184328009.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184328009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184328009 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 1, 1, 1, 1, 6, 6, 6, 6, 6, 11, 15, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 15, 15, 24, 24, 24, 24, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 21, 21, 21, 21, 21, 21, 21, 6, 6, 6, 6, 6, 6, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6] 50 rigid atoms, others: [3, 4, 5, 6] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 605) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2) `ZINC001184328009.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184328009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 77 natoms 76 natoms 75 natoms 74 names: ZINC001184328009 none CC(C)C[C@]([O-])([SiH3])C(=O)N1[C@H](COCc2ccccc2)CCC12CCN(C(=O)OC(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 3, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 6, 6, 6, 6, 10, 16, 24, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 15, 15, 26, 28, 28, 28, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 24, 24, 27, 27, 27, 27, 27, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 28, 28, 28, 28, 28, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 39, 40, 41, 42, 43, 3, 4, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73]) total number of confs: 161 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184328009 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184328009 Building ZINC001184330129 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330129 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 606) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184330129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184330129 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 40, 41, 39, 2, 3, 7, 4, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 607) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184330129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184330129 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 21, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 40, 41, 39, 2, 3, 7, 4, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184330129 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 Building ZINC001184330129 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184330129 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 606) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184330129.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184330129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184330129 none CC(C)C[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 40, 41, 39, 2, 3, 7, 4, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 607) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1) `ZINC001184330129.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184330129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184330129 none CC(C)C[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)Nc2ncc(SCc3ncc(C(C)(C)C)o3)s2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'S.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 1, 11, 8, 1, 8, 1, 1, 14, 5, 1, 8, 1, 1, 5, 5, 5, 5, 12, 14, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 21, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 33, 40, 41, 39, 2, 3, 7, 4, 6, 5] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184330129 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184330129 Building ZINC001184331853 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184331853 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 608) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])CC(C)C)c1ccccc1) `ZINC001184331853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184331853 none Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])CC(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 11, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 3, 6, 6, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [32, 64, 66, 67, 68, 69, 70, 65, 31, 30, 25, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 71, 72, 73, 74, 75]) total number of confs: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 609) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])CC(C)C)c1ccccc1) `ZINC001184331853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184331853 none Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])CC(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 10, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 3, 6, 6, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 3, 6, 6] 50 rigid atoms, others: [32, 64, 66, 67, 68, 69, 70, 65, 31, 30, 25, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 71, 72, 73, 74, 75]) total number of confs: 167 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184331853 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 Building ZINC001184331853 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184331853 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 608) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])CC(C)C)c1ccccc1) `ZINC001184331853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184331853 none Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])CC(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 11, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 3, 6, 6, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [32, 64, 66, 67, 68, 69, 70, 65, 31, 30, 25, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 71, 72, 73, 74, 75]) total number of confs: 165 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 609) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])CC(C)C)c1ccccc1) `ZINC001184331853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 79 natoms 78 natoms 77 natoms 76 names: ZINC001184331853 none Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])CC(C)C)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 45, 45, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 10, 3, 2, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 3, 6, 6, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 3, 6, 6] 50 rigid atoms, others: [32, 64, 66, 67, 68, 69, 70, 65, 31, 30, 25, 27, 28, 29, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 71, 72, 73, 74, 75]) total number of confs: 167 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184331853 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331853 Building ZINC001184331926 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184331926 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 610) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1)c1cccnc1) `ZINC001184331926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184331926 none COC(=O)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 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] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 35, 13, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 39, 39, 39, 39, 39, 35, 35, 35, 13, 13, 7, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39] 50 rigid atoms, others: [51, 56, 54, 57, 55, 50, 48, 49, 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, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60, 61, 62, 63]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 611) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1)c1cccnc1) `ZINC001184331926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184331926 none COC(=O)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 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] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 36, 13, 9, 9, 9, 9, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 47, 47, 47, 47, 47, 36, 36, 36, 13, 13, 9, 9, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 47, 47, 47] 50 rigid atoms, others: [51, 56, 54, 57, 55, 50, 48, 49, 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, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60, 61, 62, 63]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184331926 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 Building ZINC001184331926 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184331926 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 610) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1)c1cccnc1) `ZINC001184331926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184331926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184331926 none COC(=O)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@]([O-])([SiH3])CC(C)C)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 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] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 35, 13, 7, 7, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 39, 39, 39, 39, 39, 35, 35, 35, 13, 13, 7, 7, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 39, 39, 39, 39] 50 rigid atoms, others: [51, 56, 54, 57, 55, 50, 48, 49, 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, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60, 61, 62, 63]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 611) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1)c1cccnc1) `ZINC001184331926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184331926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184331926 none COC(=O)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@@]([O-])([SiH3])CC(C)C)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 8, 1, 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] dock color type numbers: [7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 34, 36, 13, 9, 9, 9, 9, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 34, 47, 47, 47, 47, 47, 36, 36, 36, 13, 13, 9, 9, 3, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 47, 47, 47, 47] 50 rigid atoms, others: [51, 56, 54, 57, 55, 50, 48, 49, 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, 16, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59, 60, 61, 62, 63]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184331926 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184331926 Building ZINC001184333034 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184333034 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 612) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184333034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184333034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184333034 none CC(C)C[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 12, 12, 7, 9, 28, 28, 29, 29, 50, 50, 28, 28, 28, 29, 29, 28, 29, 29, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 29, 29, 29, 29, 29, 29, 12, 12, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 613) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184333034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184333034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184333034 none CC(C)C[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 12, 12, 8, 10, 30, 30, 30, 30, 50, 50, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 30, 30, 30, 30, 30, 30, 12, 12, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184333034 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 Building ZINC001184333034 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184333034 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 612) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184333034.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184333034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184333034 none CC(C)C[C@@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 12, 12, 7, 9, 28, 28, 29, 29, 50, 50, 28, 28, 28, 29, 29, 28, 29, 29, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 29, 29, 29, 29, 29, 29, 12, 12, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 613) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1) `ZINC001184333034.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184333034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184333034 none CC(C)C[C@]([O-])([SiH3])C(=O)NC1(c2ccc(c3ncc(C(N)=O)cc3c3ccccc3)cc2)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 12, 12, 8, 10, 30, 30, 30, 30, 50, 50, 30, 30, 30, 30, 30, 30, 30, 30, 12, 12, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 30, 30, 30, 30, 30, 30, 12, 12, 8, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 34, 35, 36, 37, 38, 39, 40, 41, 42, 2, 3, 4, 6, 5] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184333034 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184333034 Building ZINC001184488459 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488459 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 614) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)n(c3ccccc3)n2)cc1) `ZINC001184488459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001184488459 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 10, 29, 29, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 10, 5, 5, 5, 5, 6, 6, 6, 5, 10, 10, 10, 10, 10, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 615) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)n(c3ccccc3)n2)cc1) `ZINC001184488459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001184488459 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 30, 30, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 10, 5, 5, 5, 5, 6, 6, 6, 5, 10, 10, 10, 10, 10, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488459 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 Building ZINC001184488459 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488459 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 614) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)n(c3ccccc3)n2)cc1) `ZINC001184488459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001184488459 none COc1ccc(c2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 10, 10, 29, 29, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 29, 29, 29, 29, 29, 29, 29, 10, 5, 5, 5, 5, 6, 6, 6, 5, 10, 10, 10, 10, 10, 29, 29] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 116 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 615) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)n(c3ccccc3)n2)cc1) `ZINC001184488459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 60 natoms 59 natoms 58 natoms 57 names: ZINC001184488459 none COc1ccc(c2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(OC)cc43)n(c3ccccc3)n2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 30, 30, 10, 10, 10, 5, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 6, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 30, 30, 30, 30, 30, 30, 30, 10, 5, 5, 5, 5, 6, 6, 6, 5, 10, 10, 10, 10, 10, 30, 30] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488459 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488459 Building ZINC001184488497 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488497 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 616) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)CC3)cc2)cn1) `ZINC001184488497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184488497 none Cn1cc(c2ccc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 10, 33, 33, 10, 10, 10, 10, 5, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 33, 33, 36, 36, 36, 36, 36, 36, 33, 33, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10, 33, 33, 36] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 617) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(C3CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)CC3)cc2)cn1) `ZINC001184488497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184488497 none Cn1cc(c2ccc(C3CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 34, 34, 13, 13, 13, 13, 6, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 34, 34, 38, 38, 38, 38, 38, 38, 34, 34, 13, 13, 13, 13, 13, 4, 4, 4, 4, 13, 13, 13, 13, 34, 34, 38] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488497 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 Building ZINC001184488497 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488497 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 616) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)CC3)cc2)cn1) `ZINC001184488497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184488497 none Cn1cc(c2ccc(C3CCN(C(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 10, 33, 33, 10, 10, 10, 10, 5, 2, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 10, 10, 33, 33, 36, 36, 36, 36, 36, 36, 33, 33, 10, 10, 10, 10, 10, 4, 4, 4, 4, 10, 10, 10, 10, 33, 33, 36] 50 rigid atoms, others: [16, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 617) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c2ccc(C3CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)CC3)cc2)cn1) `ZINC001184488497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184488497 none Cn1cc(c2ccc(C3CCN(C(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(Br)cc54)CC3)cc2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 13, 34, 34, 13, 13, 13, 13, 6, 1, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 13, 34, 34, 38, 38, 38, 38, 38, 38, 34, 34, 13, 13, 13, 13, 13, 4, 4, 4, 4, 13, 13, 13, 13, 34, 34, 38] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 152 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488497 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488497 Building ZINC001184488503 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488503 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 618) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)n1ncc2c1cccc2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184488503 none CC(C)(C)OC(=O)n1ncc2c1cccc2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 15, 20, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 619) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)n1ncc2c1cccc2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184488503 none CC(C)(C)OC(=O)n1ncc2c1cccc2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 15, 20, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488503 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 Building ZINC001184488503 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488503 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 618) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)n1ncc2c1cccc2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184488503 none CC(C)(C)OC(=O)n1ncc2c1cccc2NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 15, 20, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 619) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)n1ncc2c1cccc2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184488503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184488503 none CC(C)(C)OC(=O)n1ncc2c1cccc2NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 15, 20, 15, 15, 15, 15, 15, 15, 15, 15, 3, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 15, 3, 8, 8, 8, 8] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488503 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488503 Building ZINC001184488584 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488584 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 620) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)CNC(=O)OC(C)(C)C)cc3)c2c1) `ZINC001184488584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488584 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)CNC(=O)OC(C)(C)C)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 20, 20, 20, 20, 25, 26, 26, 26, 26, 26, 26, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 621) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)CNC(=O)OC(C)(C)C)cc3)c2c1) `ZINC001184488584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488584 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)CNC(=O)OC(C)(C)C)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 20, 20, 20, 20, 24, 25, 25, 25, 25, 25, 25, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488584 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 Building ZINC001184488584 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488584 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 620) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)CNC(=O)OC(C)(C)C)cc3)c2c1) `ZINC001184488584.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488584 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)CNC(=O)OC(C)(C)C)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 20, 20, 20, 20, 25, 26, 26, 26, 26, 26, 26, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 621) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)CNC(=O)OC(C)(C)C)cc3)c2c1) `ZINC001184488584.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488584 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C(C)(C)CNC(=O)OC(C)(C)C)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 3, 5, 20, 20, 20, 20, 24, 25, 25, 25, 25, 25, 25, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488584 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488584 Building ZINC001184488607 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488607 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 622) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]c3ccc(Br)cc32)c(Br)c1) `ZINC001184488607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001184488607 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 17, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 17, 17, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 26, 26, 26, 17, 17, 5, 9, 9, 9, 9, 17] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 623) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]c3ccc(Br)cc32)c(Br)c1) `ZINC001184488607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001184488607 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 17, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 26, 26, 26, 17, 17, 5, 9, 9, 9, 9, 17] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488607 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 Building ZINC001184488607 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488607 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 622) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]c3ccc(Br)cc32)c(Br)c1) `ZINC001184488607.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001184488607 none COc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 17, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 6, 17, 17, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 26, 26, 26, 17, 17, 5, 9, 9, 9, 9, 17] 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]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 623) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]c3ccc(Br)cc32)c(Br)c1) `ZINC001184488607.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 39 natoms 38 natoms 37 natoms 36 names: ZINC001184488607 none COc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', '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, 1, 17, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 17, 17, 17, 26, 26, 26, 17, 17, 5, 9, 9, 9, 9, 17] 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]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488607 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488607 Building ZINC001184488743 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488743 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 624) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F) `ZINC001184488743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184488743 none CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 16, 16, 3, 6, 6, 6, 6, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 625) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F) `ZINC001184488743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184488743 none CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 16, 16, 3, 6, 6, 6, 6, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488743 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 Building ZINC001184488743 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488743 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 624) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F) `ZINC001184488743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184488743 none CC(=O)Nc1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 16, 16, 3, 6, 6, 6, 6, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 625) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F) `ZINC001184488743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 45 natoms 44 natoms 43 natoms 42 names: ZINC001184488743 none CC(=O)Nc1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 16, 16, 16, 28, 28, 28, 28, 16, 16, 3, 6, 6, 6, 6, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488743 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488743 Building ZINC001184488623 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184488623 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/626 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 23, 25, 25, 23, 25, 25, 15, 9, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 25, 25, 23, 25, 25, 15, 15, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/627 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/627' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 24, 26, 26, 24, 26, 26, 16, 10, 3, 3, 4, 4, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 26, 26, 24, 26, 26, 16, 16, 15, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 628) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 23, 25, 25, 23, 25, 25, 15, 9, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 25, 25, 23, 25, 25, 15, 15, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 629) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 24, 26, 26, 24, 26, 26, 16, 10, 3, 3, 4, 4, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 26, 26, 24, 26, 26, 16, 16, 15, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488623 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 Building ZINC001184488623 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184488623 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 626) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 23, 25, 25, 23, 25, 25, 15, 9, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 25, 25, 23, 25, 25, 15, 15, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 627) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 24, 26, 26, 24, 26, 26, 16, 10, 3, 3, 4, 4, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 26, 26, 24, 26, 26, 16, 16, 15, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 628) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 23, 25, 25, 23, 25, 25, 15, 9, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 25, 25, 23, 25, 25, 15, 15, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 629) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 24, 26, 26, 24, 26, 26, 16, 10, 3, 3, 4, 4, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 26, 26, 24, 26, 26, 16, 16, 15, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488623 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 Building ZINC001184488623 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184488623 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 626) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 23, 25, 25, 23, 25, 25, 15, 9, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 25, 25, 23, 25, 25, 15, 15, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 627) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 24, 26, 26, 24, 26, 26, 16, 10, 3, 3, 4, 4, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 26, 26, 24, 26, 26, 16, 16, 15, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 628) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 23, 25, 25, 23, 25, 25, 15, 9, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 25, 25, 23, 25, 25, 15, 15, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 629) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 24, 26, 26, 24, 26, 26, 16, 10, 3, 3, 4, 4, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 26, 26, 24, 26, 26, 16, 16, 15, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488623 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 Building ZINC001184488623 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184488623 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 626) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 23, 25, 25, 23, 25, 25, 15, 9, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 25, 25, 23, 25, 25, 15, 15, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 627) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 24, 26, 26, 24, 26, 26, 16, 10, 3, 3, 4, 4, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 26, 26, 24, 26, 26, 16, 16, 15, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 628) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 3, 14, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 23, 25, 25, 23, 25, 25, 15, 9, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 23, 25, 25, 23, 25, 25, 25, 25, 23, 25, 25, 15, 15, 13, 13, 4] 50 rigid atoms, others: [9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 629) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1) `ZINC001184488623.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184488623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 68 natoms 67 natoms 66 natoms 65 names: ZINC001184488623 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CN(C(c5ccccc5)c5ccccc5)C4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 4, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 24, 26, 26, 24, 26, 26, 16, 10, 3, 3, 4, 4, 4, 3, 3, 3, 16, 16, 16, 16, 16, 16, 24, 27, 27, 24, 27, 27, 26, 26, 24, 26, 26, 16, 16, 15, 14, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488623 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488623 Building ZINC001184488926 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488926 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 630) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c4ccccc4oc3C(=O)c3ccc(OC)c(OC)c3)c2c1) `ZINC001184488926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184488926 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c4ccccc4oc3C(=O)c3ccc(OC)c(OC)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 31, 20, 20, 31, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 20, 20, 31, 31, 31, 31, 31, 31, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 631) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c4ccccc4oc3C(=O)c3ccc(OC)c(OC)c3)c2c1) `ZINC001184488926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184488926 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c4ccccc4oc3C(=O)c3ccc(OC)c(OC)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 31, 19, 19, 31, 19, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 19, 19, 31, 31, 31, 31, 31, 31, 19, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488926 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 Building ZINC001184488926 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184488926 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 630) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c4ccccc4oc3C(=O)c3ccc(OC)c(OC)c3)c2c1) `ZINC001184488926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184488926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184488926 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c4ccccc4oc3C(=O)c3ccc(OC)c(OC)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 20, 20, 20, 20, 31, 20, 20, 31, 20, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 20, 20, 31, 31, 31, 31, 31, 31, 20, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 631) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c4ccccc4oc3C(=O)c3ccc(OC)c(OC)c3)c2c1) `ZINC001184488926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184488926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184488926 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c4ccccc4oc3C(=O)c3ccc(OC)c(OC)c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 11, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 19, 31, 19, 19, 31, 19, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 19, 19, 31, 31, 31, 31, 31, 31, 19, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184488926 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184488926 Building ZINC001184489030 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489030 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 632) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3csc(Cc4cccc(Br)c4)n3)c2c1) `ZINC001184489030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489030 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3csc(Cc4cccc(Br)c4)n3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 30, 30, 30, 30, 30, 30, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 18, 18, 30, 30, 30, 30, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 633) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3csc(Cc4cccc(Br)c4)n3)c2c1) `ZINC001184489030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489030 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3csc(Cc4cccc(Br)c4)n3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 31, 31, 31, 31, 31, 31, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 18, 18, 31, 31, 31, 31, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489030 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 Building ZINC001184489030 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489030 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 632) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3csc(Cc4cccc(Br)c4)n3)c2c1) `ZINC001184489030.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489030 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3csc(Cc4cccc(Br)c4)n3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 30, 30, 30, 30, 30, 30, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 18, 18, 30, 30, 30, 30, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 633) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3csc(Cc4cccc(Br)c4)n3)c2c1) `ZINC001184489030.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489030 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3csc(Cc4cccc(Br)c4)n3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 14, 1, 5, 1, 1, 1, 1, 1, 17, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 18, 31, 31, 31, 31, 31, 31, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 18, 18, 31, 31, 31, 31, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489030 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489030 Building ZINC001184489309 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489309 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 634) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CC(C)(C)C)C3CCN(C(=O)OC(C)(C)C)CC3)c2c1) `ZINC001184489309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184489309 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CC(C)(C)C)C3CCN(C(=O)OC(C)(C)C)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 3, 5, 7, 7, 7, 6, 10, 10, 10, 10, 18, 18, 30, 31, 31, 31, 10, 8, 5, 5, 6, 6, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 635) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CC(C)(C)C)C3CCN(C(=O)OC(C)(C)C)CC3)c2c1) `ZINC001184489309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184489309 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CC(C)(C)C)C3CCN(C(=O)OC(C)(C)C)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 23, 24, 24, 24, 3, 3, 5, 5, 8, 8, 8, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 66 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489309 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 Building ZINC001184489309 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489309 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 634) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CC(C)(C)C)C3CCN(C(=O)OC(C)(C)C)CC3)c2c1) `ZINC001184489309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184489309 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(CC(C)(C)C)C3CCN(C(=O)OC(C)(C)C)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 3, 5, 7, 7, 7, 6, 10, 10, 10, 10, 18, 18, 30, 31, 31, 31, 10, 8, 5, 5, 6, 6, 6, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 10, 10, 10, 10, 31, 31, 31, 31, 31, 31, 31, 31, 31, 10, 10, 10, 10, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 122 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 635) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CC(C)(C)C)C3CCN(C(=O)OC(C)(C)C)CC3)c2c1) `ZINC001184489309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001184489309 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(CC(C)(C)C)C3CCN(C(=O)OC(C)(C)C)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 10, 10, 23, 24, 24, 24, 3, 3, 5, 5, 8, 8, 8, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 3, 3, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 66 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489309 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489309 Building ZINC001184489342 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489342 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 636) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Br)cc3OC(F)(F)F)c2c1) `ZINC001184489342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184489342 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Br)cc3OC(F)(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 11, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 637) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Br)cc3OC(F)(F)F)c2c1) `ZINC001184489342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184489342 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Br)cc3OC(F)(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 11, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489342 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 Building ZINC001184489342 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489342 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 636) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Br)cc3OC(F)(F)F)c2c1) `ZINC001184489342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184489342 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(Br)cc3OC(F)(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 11, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 637) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Br)cc3OC(F)(F)F)c2c1) `ZINC001184489342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184489342 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(Br)cc3OC(F)(F)F)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 17, 1, 1, 12, 5, 15, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 11, 11, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 11, 5] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489342 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489342 Building ZINC001184489532 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489532 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 638) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(n4c5ccccc5nc4C(F)(F)F)CC3)c2c1) `ZINC001184489532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489532 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(n4c5ccccc5nc4C(F)(F)F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 9, 14, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 5, 5, 6, 6, 6, 5, 5, 5, 14, 14, 14, 14, 14, 23, 23, 23, 23, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 48 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 639) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(n4c5ccccc5nc4C(F)(F)F)CC3)c2c1) `ZINC001184489532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489532 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(n4c5ccccc5nc4C(F)(F)F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 4, 8, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 20, 20, 20, 20, 12, 12, 12, 12, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489532 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 Building ZINC001184489532 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489532 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 638) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(n4c5ccccc5nc4C(F)(F)F)CC3)c2c1) `ZINC001184489532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489532 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC(n4c5ccccc5nc4C(F)(F)F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 5, 9, 14, 14, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 5, 5, 6, 6, 6, 5, 5, 5, 14, 14, 14, 14, 14, 23, 23, 23, 23, 14, 14, 14, 14, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 48 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 639) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(n4c5ccccc5nc4C(F)(F)F)CC3)c2c1) `ZINC001184489532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489532 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC(n4c5ccccc5nc4C(F)(F)F)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 15, 15, 15, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 4, 8, 12, 12, 12, 12, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 12, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 20, 20, 20, 20, 12, 12, 12, 12, 6] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489532 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489532 Building ZINC001184489830 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489830 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/640 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 29, 29, 27, 29, 29, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27, 29, 29, 27, 29, 29, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/641 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/641' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 24, 30, 30, 24, 30, 30, 7, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 24, 24, 30, 30, 24, 30, 30, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 642) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 29, 29, 27, 29, 29, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27, 29, 29, 27, 29, 29, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 643) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 24, 30, 30, 24, 30, 30, 7, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 24, 24, 30, 30, 24, 30, 30, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489830 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 Building ZINC001184489830 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489830 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 640) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 29, 29, 27, 29, 29, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27, 29, 29, 27, 29, 29, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 641) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 24, 30, 30, 24, 30, 30, 7, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 24, 24, 30, 30, 24, 30, 30, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 642) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 29, 29, 27, 29, 29, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27, 29, 29, 27, 29, 29, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 643) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 24, 30, 30, 24, 30, 30, 7, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 24, 24, 30, 30, 24, 30, 30, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489830 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 Building ZINC001184489830 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489830 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 640) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 29, 29, 27, 29, 29, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27, 29, 29, 27, 29, 29, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 641) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 24, 30, 30, 24, 30, 30, 7, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 24, 24, 30, 30, 24, 30, 30, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 642) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 29, 29, 27, 29, 29, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27, 29, 29, 27, 29, 29, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 643) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 24, 30, 30, 24, 30, 30, 7, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 24, 24, 30, 30, 24, 30, 30, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489830 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 Building ZINC001184489830 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489830 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 640) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 29, 29, 27, 29, 29, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27, 29, 29, 27, 29, 29, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 641) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 24, 30, 30, 24, 30, 30, 7, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 24, 24, 30, 30, 24, 30, 30, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 642) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 7, 27, 29, 29, 27, 29, 29, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 27, 27, 29, 29, 27, 29, 29, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 643) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489830.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489830 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 7, 7, 7, 7, 7, 24, 30, 30, 24, 30, 30, 7, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 24, 24, 30, 30, 24, 30, 30, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 133 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489830 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489830 Building ZINC001184489832 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489832 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/644 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 6, 7, 7, 7, 7, 23, 25, 25, 24, 25, 25, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/645 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/645' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 20, 26, 26, 23, 26, 26, 5, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 20, 20, 26, 26, 26, 26, 26, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 646) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 6, 7, 7, 7, 7, 23, 25, 25, 24, 25, 25, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 647) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 20, 26, 26, 23, 26, 26, 5, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 20, 20, 26, 26, 26, 26, 26, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489832 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 Building ZINC001184489832 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489832 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 644) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 6, 7, 7, 7, 7, 23, 25, 25, 24, 25, 25, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 645) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 20, 26, 26, 23, 26, 26, 5, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 20, 20, 26, 26, 26, 26, 26, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 646) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 6, 7, 7, 7, 7, 23, 25, 25, 24, 25, 25, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 647) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 20, 26, 26, 23, 26, 26, 5, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 20, 20, 26, 26, 26, 26, 26, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489832 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 Building ZINC001184489832 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489832 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 644) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 6, 7, 7, 7, 7, 23, 25, 25, 24, 25, 25, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 645) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 20, 26, 26, 23, 26, 26, 5, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 20, 20, 26, 26, 26, 26, 26, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 646) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 6, 7, 7, 7, 7, 23, 25, 25, 24, 25, 25, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 647) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 20, 26, 26, 23, 26, 26, 5, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 20, 20, 26, 26, 26, 26, 26, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489832 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 Building ZINC001184489832 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184489832 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 644) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 6, 7, 7, 7, 7, 23, 25, 25, 24, 25, 25, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 645) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 20, 26, 26, 23, 26, 26, 5, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 20, 20, 26, 26, 26, 26, 26, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 646) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 6, 7, 7, 7, 7, 23, 25, 25, 24, 25, 25, 7, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 7, 23, 23, 25, 25, 25, 25, 25, 7, 7, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 111 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 647) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1) `ZINC001184489832.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184489832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 67 natoms 66 natoms 65 natoms 64 names: ZINC001184489832 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(Cc3ccccc3)[C@H]3CCN(Cc4ccccc4)C3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 5, 7, 5, 5, 10, 5, 1, 1, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 4, 4, 3, 5, 5, 5, 5, 5, 20, 26, 26, 23, 26, 26, 5, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 20, 20, 26, 26, 26, 26, 26, 5, 5, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489832 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489832 Building ZINC001184489840 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489840 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 648) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@H]3C(OC)(c3ccccc3)c3ccccc3)c2c1) `ZINC001184489840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489840 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@H]3C(OC)(c3ccccc3)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 13, 19, 13, 15, 15, 14, 15, 15, 13, 14, 14, 13, 14, 14, 6, 6, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 15, 15, 14, 15, 15, 14, 14, 13, 14, 14, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 80 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 649) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@H]3C(OC)(c3ccccc3)c3ccccc3)c2c1) `ZINC001184489840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489840 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@H]3C(OC)(c3ccccc3)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 15, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 8, 8, 8, 5, 5, 5, 8, 8, 8, 8, 8, 8, 22, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 29 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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: 74 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489840 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 Building ZINC001184489840 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489840 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 648) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@H]3C(OC)(c3ccccc3)c3ccccc3)c2c1) `ZINC001184489840.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489840 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC[C@H]3C(OC)(c3ccccc3)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 13, 19, 13, 15, 15, 14, 15, 15, 13, 14, 14, 13, 14, 14, 6, 6, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 15, 15, 14, 15, 15, 14, 14, 13, 14, 14, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 80 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 649) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@H]3C(OC)(c3ccccc3)c3ccccc3)c2c1) `ZINC001184489840.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184489840 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC[C@H]3C(OC)(c3ccccc3)c3ccccc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 15, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 8, 8, 8, 5, 5, 5, 8, 8, 8, 8, 8, 8, 22, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5] 29 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 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: 74 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489840 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489840 Building ZINC001184489882 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489882 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 650) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)c3ccccc3CN4C(=O)OC(C)(C)C)c2c1) `ZINC001184489882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489882 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)c3ccccc3CN4C(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 6, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 651) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)c3ccccc3CN4C(=O)OC(C)(C)C)c2c1) `ZINC001184489882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489882 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)c3ccccc3CN4C(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 27, 27, 27, 27, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489882 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 Building ZINC001184489882 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489882 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 650) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)c3ccccc3CN4C(=O)OC(C)(C)C)c2c1) `ZINC001184489882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489882 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N3CCC4(CC3)c3ccccc3CN4C(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 6, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 23, 23, 27, 27, 27, 27, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 27, 27, 27, 27, 27, 27, 27, 27, 27, 5] 50 rigid atoms, others: [9, 10, 11] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 651) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)c3ccccc3CN4C(=O)OC(C)(C)C)c2c1) `ZINC001184489882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 70 natoms 69 natoms 68 natoms 67 names: ZINC001184489882 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N3CCC4(CC3)c3ccccc3CN4C(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 12, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 5, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 21, 21, 27, 27, 27, 27, 4, 4, 5, 5, 5, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489882 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489882 Building ZINC001184489934 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489934 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 652) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(OC)cccc3c3cc(=O)c4ccccc4o3)c2c1) `ZINC001184489934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489934 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(OC)cccc3c3cc(=O)c4ccccc4o3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 12, 14, 12, 5, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 7, 7, 7, 6, 6, 6, 3, 14, 14, 14, 12, 12, 12, 29, 29, 29, 29, 29, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 653) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(OC)cccc3c3cc(=O)c4ccccc4o3)c2c1) `ZINC001184489934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489934 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(OC)cccc3c3cc(=O)c4ccccc4o3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 15, 14, 7, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 15, 14, 14, 14, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489934 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 Building ZINC001184489934 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489934 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 652) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(OC)cccc3c3cc(=O)c4ccccc4o3)c2c1) `ZINC001184489934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489934 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3c(OC)cccc3c3cc(=O)c4ccccc4o3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 12, 12, 14, 12, 5, 12, 12, 12, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 7, 7, 7, 6, 6, 6, 3, 14, 14, 14, 12, 12, 12, 29, 29, 29, 29, 29, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 653) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(OC)cccc3c3cc(=O)c4ccccc4o3)c2c1) `ZINC001184489934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184489934 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3c(OC)cccc3c3cc(=O)c4ccccc4o3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 11, 1, 1, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 4, 4, 4, 14, 14, 15, 14, 7, 14, 14, 14, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 6, 6, 6, 6, 6, 6, 6, 6, 4, 15, 15, 15, 14, 14, 14, 31, 31, 31, 31, 31, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489934 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489934 Building ZINC001184489985 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489985 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 654) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)cc3C(=O)c3ccc(Cl)cc3)c2c1) `ZINC001184489985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489985 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)cc3C(=O)c3ccc(Cl)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 14, 11, 11, 11, 17, 17, 18, 18, 17, 17, 18, 18, 7, 7, 9, 9, 9, 7, 7, 7, 5, 11, 11, 14, 14, 14, 11, 18, 18, 18, 18, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 655) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)cc3C(=O)c3ccc(Cl)cc3)c2c1) `ZINC001184489985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489985 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)cc3C(=O)c3ccc(Cl)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 15, 11, 11, 11, 17, 17, 18, 18, 17, 17, 18, 18, 7, 7, 9, 9, 9, 7, 7, 7, 5, 11, 11, 15, 15, 15, 11, 18, 18, 18, 18, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489985 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 Building ZINC001184489985 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184489985 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 654) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)cc3C(=O)c3ccc(Cl)cc3)c2c1) `ZINC001184489985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184489985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489985 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(OC)cc3C(=O)c3ccc(Cl)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 14, 11, 11, 11, 17, 17, 18, 18, 17, 17, 18, 18, 7, 7, 9, 9, 9, 7, 7, 7, 5, 11, 11, 14, 14, 14, 11, 18, 18, 18, 18, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 655) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)cc3C(=O)c3ccc(Cl)cc3)c2c1) `ZINC001184489985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184489985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184489985 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(OC)cc3C(=O)c3ccc(Cl)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.2', '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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 11, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 15, 11, 11, 11, 17, 17, 18, 18, 17, 17, 18, 18, 7, 7, 9, 9, 9, 7, 7, 7, 5, 11, 11, 15, 15, 15, 11, 18, 18, 18, 18, 7] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184489985 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184489985 Building ZINC001184490104 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490104 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 656) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1ccccc1)S(=O)(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)ccc1C) `ZINC001184490104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184490104 none CCN(c1ccccc1)S(=O)(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 18, 29, 29, 29, 29, 29, 29, 8, 18, 18, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 3, 3, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 8, 3, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 657) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1ccccc1)S(=O)(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)ccc1C) `ZINC001184490104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184490104 none CCN(c1ccccc1)S(=O)(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 18, 29, 29, 29, 29, 29, 29, 8, 18, 18, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 3, 3, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 8, 3, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490104 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 Building ZINC001184490104 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490104 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 656) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1ccccc1)S(=O)(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)ccc1C) `ZINC001184490104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184490104 none CCN(c1ccccc1)S(=O)(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 18, 29, 29, 29, 29, 29, 29, 8, 18, 18, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 3, 3, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 8, 3, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 657) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(c1ccccc1)S(=O)(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)ccc1C) `ZINC001184490104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184490104 none CCN(c1ccccc1)S(=O)(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)ccc1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', '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'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 14, 11, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 29, 18, 29, 29, 29, 29, 29, 29, 8, 18, 18, 8, 8, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 3, 3, 30, 30, 30, 30, 30, 29, 29, 29, 29, 29, 8, 3, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 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]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490104 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490104 Building ZINC001184490398 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490398 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/658 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 39, 42, 42, 40, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 39, 39, 42, 42, 42, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/659 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/659' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 38, 42, 42, 38, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 38, 38, 42, 42, 38, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 660) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 39, 42, 42, 40, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 39, 39, 42, 42, 42, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 661) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 38, 42, 42, 38, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 38, 38, 42, 42, 38, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490398 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 Building ZINC001184490398 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490398 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 658) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 39, 42, 42, 42, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 39, 39, 42, 42, 42, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 659) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 38, 42, 42, 38, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 38, 38, 42, 42, 38, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 660) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 39, 42, 42, 40, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 39, 39, 42, 42, 42, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 661) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 38, 42, 42, 38, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 38, 38, 42, 42, 38, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490398 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 Building ZINC001184490398 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490398 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 658) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 39, 42, 42, 42, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 39, 39, 42, 42, 42, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 659) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 38, 42, 42, 38, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 38, 38, 42, 42, 38, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 660) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 39, 42, 42, 40, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 39, 39, 42, 42, 42, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 661) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 38, 42, 42, 38, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 38, 38, 42, 42, 38, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490398 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 Building ZINC001184490398 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184490398 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 658) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 39, 42, 42, 42, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 39, 39, 42, 42, 42, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 177 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 659) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 38, 42, 42, 38, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 38, 38, 42, 42, 38, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 660) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 39, 42, 42, 40, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 39, 39, 42, 42, 42, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 187 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 661) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1) `ZINC001184490398.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184490398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 69 natoms 68 natoms 67 natoms 66 names: ZINC001184490398 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)N(c3ccccc3N)[C@H]3CC[N@@](Cc4ccccc4)CC3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 3, 4, 4, 3, 4, 4, 4, 3, 21, 21, 21, 21, 21, 38, 42, 42, 38, 42, 42, 21, 21, 3, 3, 4, 4, 4, 3, 3, 3, 4, 4, 4, 4, 4, 4, 21, 21, 21, 21, 38, 38, 42, 42, 38, 42, 42, 21, 21, 21, 21, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490398 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490398 Building ZINC001184490835 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490835 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 662) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc([C@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1) `ZINC001184490835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490835 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc([C@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 29, 29, 29, 29, 29, 38, 38, 38, 38, 38, 38, 29, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 29, 29, 29, 29, 38, 38, 38, 38, 38, 38, 38, 38, 38, 29, 29, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 663) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc([C@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1) `ZINC001184490835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490835 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc([C@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 26, 26, 26, 26, 26, 35, 35, 35, 35, 35, 35, 26, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 26, 26, 26, 26, 35, 35, 35, 35, 35, 35, 35, 35, 35, 26, 26, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490835 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 Building ZINC001184490835 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490835 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 662) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc([C@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1) `ZINC001184490835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490835 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc([C@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 29, 29, 29, 29, 29, 38, 38, 38, 38, 38, 38, 29, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 29, 29, 29, 29, 38, 38, 38, 38, 38, 38, 38, 38, 38, 29, 29, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 113 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 663) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc([C@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1) `ZINC001184490835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490835 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc([C@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 26, 26, 26, 26, 26, 35, 35, 35, 35, 35, 35, 26, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 26, 26, 26, 26, 35, 35, 35, 35, 35, 35, 35, 35, 35, 26, 26, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490835 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490835 Building ZINC001184490836 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490836 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 664) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc([C@@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1) `ZINC001184490836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490836 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc([C@@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 26, 26, 26, 26, 26, 36, 36, 36, 36, 36, 36, 26, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 26, 26, 26, 26, 36, 36, 36, 36, 36, 36, 36, 36, 36, 26, 26, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 665) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc([C@@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1) `ZINC001184490836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490836 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc([C@@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 28, 28, 28, 28, 28, 36, 36, 36, 36, 36, 36, 28, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 28, 28, 28, 28, 36, 36, 36, 36, 36, 36, 36, 36, 36, 28, 28, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490836 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 Building ZINC001184490836 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184490836 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 664) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc([C@@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1) `ZINC001184490836.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184490836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490836 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc([C@@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 26, 26, 26, 26, 26, 36, 36, 36, 36, 36, 36, 26, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 26, 26, 26, 26, 36, 36, 36, 36, 36, 36, 36, 36, 36, 26, 26, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 665) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc([C@@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1) `ZINC001184490836.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184490836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184490836 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc([C@@H]4CCN(C(=O)OC(C)(C)C)C4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 7, 5, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 8, 28, 28, 28, 28, 28, 36, 36, 36, 36, 36, 36, 28, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 28, 28, 28, 28, 36, 36, 36, 36, 36, 36, 36, 36, 36, 28, 28, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184490836 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184490836 Building ZINC001184491166 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491166 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 666) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1csc2nc(c3cccc(NC(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)c3)cn12) `ZINC001184491166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184491166 none CCOC(=O)c1csc2nc(c3cccc(NC(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)c3)cn12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', '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, 14, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 20, 24, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 20, 20, 27, 27, 27, 27, 27, 20, 8, 8, 8, 4, 4, 4, 4, 5, 5, 5, 4, 8, 20] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 667) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1csc2nc(c3cccc(NC(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)c3)cn12) `ZINC001184491166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184491166 none CCOC(=O)c1csc2nc(c3cccc(NC(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)c3)cn12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', '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, 14, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 25, 19, 25, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 19, 19, 28, 28, 28, 28, 28, 19, 7, 7, 7, 3, 4, 4, 4, 5, 5, 5, 4, 7, 19] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491166 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 Building ZINC001184491166 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491166 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 666) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1csc2nc(c3cccc(NC(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)c3)cn12) `ZINC001184491166.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184491166 none CCOC(=O)c1csc2nc(c3cccc(NC(=O)[C@@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)c3)cn12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', '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, 14, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 24, 24, 20, 24, 20, 20, 20, 20, 20, 8, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 8, 20, 20, 27, 27, 27, 27, 27, 20, 8, 8, 8, 4, 4, 4, 4, 5, 5, 5, 4, 8, 20] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 667) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1csc2nc(c3cccc(NC(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)c3)cn12) `ZINC001184491166.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184491166 none CCOC(=O)c1csc2nc(c3cccc(NC(=O)[C@]([O-])([SiH3])c4c[nH]c5ccc(OC)cc54)c3)cn12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'H', '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, 14, 1, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 25, 25, 19, 25, 19, 19, 19, 19, 19, 7, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 5, 4, 4, 7, 19, 19, 28, 28, 28, 28, 28, 19, 7, 7, 7, 3, 4, 4, 4, 5, 5, 5, 4, 7, 19] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491166 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491166 Building ZINC001184491173 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491173 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 668) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(NC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184491173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491173 none CCOC(=O)c1cc(NC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 12, 9, 9, 9, 9, 14, 22, 22, 27, 27, 27, 27, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 12, 12, 12, 12, 12, 9, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 3, 4, 4, 4, 4, 4, 4, 4, 9] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 669) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(NC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184491173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491173 none CCOC(=O)c1cc(NC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 9, 12, 9, 9, 9, 9, 14, 21, 21, 25, 25, 25, 25, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 13, 13, 13, 13, 13, 9, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 3, 4, 4, 4, 4, 4, 4, 4, 9] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491173 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 Building ZINC001184491173 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491173 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 668) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(NC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184491173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491173 none CCOC(=O)c1cc(NC(=O)OC(C)(C)C)cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 12, 9, 9, 9, 9, 14, 22, 22, 27, 27, 27, 27, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 12, 12, 12, 12, 12, 9, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 9, 3, 4, 4, 4, 4, 4, 4, 4, 9] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 669) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1cc(NC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1) `ZINC001184491173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC001184491173 none CCOC(=O)c1cc(NC(=O)OC(C)(C)C)cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(OC)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 12, 12, 9, 12, 9, 9, 9, 9, 14, 21, 21, 25, 25, 25, 25, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 13, 13, 13, 13, 13, 9, 14, 25, 25, 25, 25, 25, 25, 25, 25, 25, 9, 3, 4, 4, 4, 4, 4, 4, 4, 9] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491173 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491173 Building ZINC001184491354 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491354 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 670) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4sc(NC(=O)OC(C)(C)C)nc4c3)c2c1) `ZINC001184491354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184491354 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4sc(NC(=O)OC(C)(C)C)nc4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 671) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4sc(NC(=O)OC(C)(C)C)nc4c3)c2c1) `ZINC001184491354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184491354 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4sc(NC(=O)OC(C)(C)C)nc4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 27, 27, 27, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491354 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 Building ZINC001184491354 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491354 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 670) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4sc(NC(=O)OC(C)(C)C)nc4c3)c2c1) `ZINC001184491354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184491354 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc4sc(NC(=O)OC(C)(C)C)nc4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 24, 24, 24, 24, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 14, 24, 24, 24, 24, 24, 24, 24, 24, 24, 14, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 671) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4sc(NC(=O)OC(C)(C)C)nc4c3)c2c1) `ZINC001184491354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184491354 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc4sc(NC(=O)OC(C)(C)C)nc4c3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 14, 1, 8, 1, 11, 12, 5, 5, 5, 5, 8, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 3, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 25, 27, 27, 27, 14, 14, 14, 6, 6, 6, 6, 6, 6, 6, 6, 3, 14, 14, 14, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 6] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491354 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491354 Building ZINC001184491363 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491363 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 672) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C4(NC(=O)OC(C)(C)C)CCC4)cc3)c2c1) `ZINC001184491363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491363 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C4(NC(=O)OC(C)(C)C)CCC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 9, 21, 21, 29, 29, 29, 29, 29, 29, 21, 21, 21, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 673) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C4(NC(=O)OC(C)(C)C)CCC4)cc3)c2c1) `ZINC001184491363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491363 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C4(NC(=O)OC(C)(C)C)CCC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 8, 20, 21, 29, 29, 29, 29, 29, 29, 20, 20, 20, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 20, 20, 21, 20, 20, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491363 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 Building ZINC001184491363 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184491363 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 672) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C4(NC(=O)OC(C)(C)C)CCC4)cc3)c2c1) `ZINC001184491363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491363 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3ccc(C4(NC(=O)OC(C)(C)C)CCC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 9, 21, 21, 29, 29, 29, 29, 29, 29, 21, 21, 21, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 21, 21, 21, 21, 21, 21, 5, 5, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 673) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C4(NC(=O)OC(C)(C)C)CCC4)cc3)c2c1) `ZINC001184491363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 66 natoms 65 natoms 64 natoms 63 names: ZINC001184491363 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3ccc(C4(NC(=O)OC(C)(C)C)CCC4)cc3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 5, 8, 1, 11, 12, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 3, 8, 20, 21, 29, 29, 29, 29, 29, 29, 20, 20, 20, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 21, 29, 29, 29, 29, 29, 29, 29, 29, 29, 20, 20, 20, 21, 20, 20, 7, 7, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491363 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491363 Building ZINC001184491365 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491365 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/674 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 11, 11, 11, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/675 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/675' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 14, 14, 14, 9, 9, 9, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 676) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 11, 11, 11, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 677) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 14, 14, 14, 9, 9, 9, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491365 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 Building ZINC001184491365 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491365 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 674) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 11, 11, 11, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 675) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 14, 14, 14, 9, 9, 9, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 676) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 11, 11, 11, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 677) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 14, 14, 14, 9, 9, 9, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491365 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 Building ZINC001184491365 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491365 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 674) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 11, 11, 11, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 675) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 14, 14, 14, 9, 9, 9, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 676) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 11, 11, 11, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 677) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 14, 14, 14, 9, 9, 9, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491365 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 Building ZINC001184491365 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491365 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 674) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 11, 11, 11, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 675) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 14, 14, 14, 9, 9, 9, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 676) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 11, 11, 11, 8, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 677) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491365.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491365 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 14, 14, 14, 9, 9, 9, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491365 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491365 Building ZINC001184491366 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491366 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/678 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 13, 13, 13, 9, 9, 9, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/679 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/679' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 51 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 680) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 13, 13, 13, 9, 9, 9, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 681) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 51 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491366 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 Building ZINC001184491366 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491366 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 678) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 13, 13, 13, 9, 9, 9, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 679) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 51 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 680) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 13, 13, 13, 9, 9, 9, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 681) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 51 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491366 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 Building ZINC001184491366 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491366 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 678) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 13, 13, 13, 9, 9, 9, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 679) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 51 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 680) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 13, 13, 13, 9, 9, 9, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 681) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 51 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491366 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 Building ZINC001184491366 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184491366 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 678) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 13, 13, 13, 9, 9, 9, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 679) grep: /scratch/xiaobo/281161/xco-8058088.67/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: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 51 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 680) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 6, 6, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 13, 13, 13, 9, 9, 9, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 50 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 681) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1) `ZINC001184491366.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184491366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184491366 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3cccc4c3[C@@H]3Cc5ccccc5CN3CC4)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 7, 5, 1, 1, 1, 1, 1, 1, 5, 10, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 6, 6, 8, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 8, 11, 11, 11, 8, 8, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 51 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184491366 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184491366 Building ZINC001184492562 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184492562 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 682) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCSc3cc(C(F)(F)F)nc4ccccc43)c2c1) `ZINC001184492562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184492562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184492562 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCSc3cc(C(F)(F)F)nc4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 8, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 8, 8, 38, 38, 38, 38, 38, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 683) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCSc3cc(C(F)(F)F)nc4ccccc43)c2c1) `ZINC001184492562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184492562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184492562 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCSc3cc(C(F)(F)F)nc4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 8, 18, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 8, 8, 39, 39, 39, 39, 39, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184492562 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 Building ZINC001184492562 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184492562 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 682) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCSc3cc(C(F)(F)F)nc4ccccc43)c2c1) `ZINC001184492562.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184492562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184492562 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCCSc3cc(C(F)(F)F)nc4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 8, 18, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 8, 8, 38, 38, 38, 38, 38, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 683) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCSc3cc(C(F)(F)F)nc4ccccc43)c2c1) `ZINC001184492562.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184492562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184492562 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCCSc3cc(C(F)(F)F)nc4ccccc43)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.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'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 5, 14, 1, 1, 1, 5, 15, 15, 15, 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] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 6, 8, 18, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 8, 8, 39, 39, 39, 39, 39, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184492562 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184492562 Building ZINC001184494702 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184494702 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 684) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1) `ZINC001184494702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184494702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184494702 none CCn1c2ccccc2nc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 5, 7, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 6, 6, 7, 12, 12, 7, 12, 12, 22, 22, 22, 22, 22, 20, 20, 20, 20, 5, 6, 6, 6, 8, 8, 8, 6, 12, 12, 7, 12, 12] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 685) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1) `ZINC001184494702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184494702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184494702 none CCn1c2ccccc2nc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 6, 6, 5, 10, 10, 5, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 6, 10, 10, 10, 6, 10, 10, 5, 10, 10] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184494702 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 Building ZINC001184494702 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184494702 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 684) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1) `ZINC001184494702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184494702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184494702 none CCn1c2ccccc2nc1[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 5, 7, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 6, 6, 7, 12, 12, 7, 12, 12, 22, 22, 22, 22, 22, 20, 20, 20, 20, 5, 6, 6, 6, 8, 8, 8, 6, 12, 12, 7, 12, 12] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 685) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1) `ZINC001184494702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184494702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184494702 none CCn1c2ccccc2nc1[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 6, 6, 5, 10, 10, 5, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 6, 10, 10, 10, 6, 10, 10, 5, 10, 10] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184494702 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494702 Building ZINC001184494703 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184494703 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 686) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1) `ZINC001184494703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184494703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184494703 none CCn1c2ccccc2nc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 6, 6, 5, 11, 11, 5, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 6, 10, 10, 10, 6, 11, 11, 5, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 687) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1) `ZINC001184494703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184494703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184494703 none CCn1c2ccccc2nc1[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 5, 7, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 6, 6, 7, 12, 12, 7, 12, 12, 22, 22, 22, 22, 22, 20, 20, 20, 20, 5, 6, 6, 6, 8, 8, 8, 6, 12, 12, 7, 12, 12] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184494703 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 Building ZINC001184494703 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184494703 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 686) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1) `ZINC001184494703.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184494703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184494703 none CCn1c2ccccc2nc1[C@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 3, 5, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 10, 6, 6, 5, 11, 11, 5, 11, 11, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 6, 6, 6, 10, 10, 10, 6, 11, 11, 5, 11, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 687) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1c2ccccc2nc1[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1) `ZINC001184494703.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184494703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC001184494703 none CCn1c2ccccc2nc1[C@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(OC)cc21)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.2', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 1, 8, 1, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 20, 20, 20, 20, 20, 20, 20, 20, 7, 5, 7, 5, 1, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 8, 6, 6, 7, 12, 12, 7, 12, 12, 22, 22, 22, 22, 22, 20, 20, 20, 20, 5, 6, 6, 6, 8, 8, 8, 6, 12, 12, 7, 12, 12] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184494703 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184494703 Building ZINC001184495244 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184495244 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 688) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3coc(c4ccc(OCc5ccccc5)cc4)n3)c2c1) `ZINC001184495244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184495244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184495244 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3coc(c4ccc(OCc5ccccc5)cc4)n3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 28, 28, 23, 23, 39, 39, 39, 39, 39, 39, 39, 28, 28, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 16, 28, 28, 39, 39, 39, 39, 39, 39, 39, 28, 28, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 689) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3coc(c4ccc(OCc5ccccc5)cc4)n3)c2c1) `ZINC001184495244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184495244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184495244 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3coc(c4ccc(OCc5ccccc5)cc4)n3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 28, 28, 23, 23, 39, 39, 39, 39, 39, 39, 39, 28, 28, 16, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 16, 28, 28, 39, 39, 39, 39, 39, 39, 39, 28, 28, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184495244 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 Building ZINC001184495244 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184495244 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 688) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3coc(c4ccc(OCc5ccccc5)cc4)n3)c2c1) `ZINC001184495244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184495244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184495244 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)NCc3coc(c4ccc(OCc5ccccc5)cc4)n3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 16, 16, 16, 16, 28, 28, 23, 23, 39, 39, 39, 39, 39, 39, 39, 28, 28, 16, 3, 3, 3, 3, 3, 3, 3, 3, 2, 8, 8, 16, 28, 28, 39, 39, 39, 39, 39, 39, 39, 28, 28, 3] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 689) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3coc(c4ccc(OCc5ccccc5)cc4)n3)c2c1) `ZINC001184495244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184495244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184495244 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)NCc3coc(c4ccc(OCc5ccccc5)cc4)n3)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 12, 1, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 7, 16, 16, 16, 16, 28, 28, 23, 23, 39, 39, 39, 39, 39, 39, 39, 28, 28, 16, 2, 2, 2, 2, 2, 2, 2, 2, 1, 7, 7, 16, 28, 28, 39, 39, 39, 39, 39, 39, 39, 28, 28, 2] 50 rigid atoms, others: [43, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184495244 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184495244 Building ZINC001184477741 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477741 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 690) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Cl)c1OC(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184477741 none O=C(Nc1ccnc(Cl)c1OC(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 16, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 15, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 9, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 691) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Cl)c1OC(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184477741 none O=C(Nc1ccnc(Cl)c1OC(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 16, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 16, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 10, 10, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184477741 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 Building ZINC001184477741 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477741 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 690) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Cl)c1OC(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184477741 none O=C(Nc1ccnc(Cl)c1OC(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 16, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 9, 9, 9, 9, 9, 9, 9, 15, 19, 19, 19, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 9, 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]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 691) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnc(Cl)c1OC(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001184477741 none O=C(Nc1ccnc(Cl)c1OC(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 1, 16, 1, 12, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 10, 10, 10, 10, 10, 10, 10, 16, 20, 20, 20, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 10, 10, 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]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184477741 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477741 Building ZINC001184477818 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477818 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 692) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cc(c2ccccc2)sc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184477818 none NC(=O)c1cc(c2ccccc2)sc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 0 hydrogens 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, 25, 25, 11, 25, 25, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 25, 25, 11, 25, 25, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 693) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cc(c2ccccc2)sc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184477818 none NC(=O)c1cc(c2ccccc2)sc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 0 hydrogens 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, 27, 27, 11, 27, 27, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 27, 27, 11, 27, 27, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184477818 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 Building ZINC001184477818 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477818 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 692) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cc(c2ccccc2)sc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477818.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184477818 none NC(=O)c1cc(c2ccccc2)sc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 0 hydrogens 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, 25, 25, 11, 25, 25, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 25, 25, 11, 25, 25, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 693) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1cc(c2ccccc2)sc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477818.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184477818 none NC(=O)c1cc(c2ccccc2)sc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 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] 0 hydrogens 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, 27, 27, 11, 27, 27, 11, 4, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 27, 27, 11, 27, 27, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 83 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184477818 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477818 Building ZINC001184477881 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477881 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 694) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1sc(c2ccsc2)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184477881 none NC(=O)c1sc(c2ccsc2)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 14, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 9, 9, 9, 9, 32, 32, 32, 32, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 9, 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]) total number of confs: 58 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 695) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1sc(c2ccsc2)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184477881 none NC(=O)c1sc(c2ccsc2)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 14, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 9, 9, 9, 9, 32, 32, 32, 32, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 9, 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]) total number of confs: 58 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184477881 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 Building ZINC001184477881 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184477881 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 694) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1sc(c2ccsc2)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184477881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184477881 none NC(=O)c1sc(c2ccsc2)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 14, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 9, 9, 9, 9, 32, 32, 32, 32, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 9, 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]) total number of confs: 58 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 695) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC(=O)c1sc(c2ccsc2)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184477881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184477881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184477881 none NC(=O)c1sc(c2ccsc2)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 11, 1, 14, 1, 1, 1, 1, 14, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 11, 9, 9, 9, 9, 32, 32, 32, 32, 9, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 32, 32, 32, 9, 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]) total number of confs: 58 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184477881 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184477881 Building ZINC001184478382 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478382 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 696) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c[nH]c2ccc(Br)cc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184478382 none O=C(Nc1c[nH]c2ccc(Br)cc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 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, 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: [6, 1, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 19, 19, 19, 19, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 697) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c[nH]c2ccc(Br)cc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184478382 none O=C(Nc1c[nH]c2ccc(Br)cc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 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, 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: [6, 1, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 19, 19, 19, 19, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184478382 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 Building ZINC001184478382 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478382 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 696) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c[nH]c2ccc(Br)cc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478382.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184478382 none O=C(Nc1c[nH]c2ccc(Br)cc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 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, 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: [6, 1, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 19, 19, 19, 19, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 697) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1c[nH]c2ccc(Br)cc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184478382.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184478382 none O=C(Nc1c[nH]c2ccc(Br)cc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 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, 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: [6, 1, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 19, 19, 19, 19, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184478382 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478382 Building ZINC001184478462 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478462 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 698) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]c3ccc(Br)cc32)nc(C)c1Br) `ZINC001184478462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001184478462 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc(C)c1Br 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 1, 17, 1, 1, 8, 1, 5, 1, 17, 7, 7, 7, 7, 6, 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, 3, 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: [18, 18, 18, 11, 11, 1, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 9, 9, 9, 9, 18, 18, 18] 46 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]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 699) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]c3ccc(Br)cc32)nc(C)c1Br) `ZINC001184478462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001184478462 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc(C)c1Br 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 1, 17, 1, 1, 8, 1, 5, 1, 17, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 11, 1, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 9, 9, 9, 9, 18, 18, 18] 47 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]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184478462 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 Building ZINC001184478462 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184478462 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 698) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]c3ccc(Br)cc32)nc(C)c1Br) `ZINC001184478462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184478462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001184478462 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc(C)c1Br 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 1, 17, 1, 1, 8, 1, 5, 1, 17, 7, 7, 7, 7, 6, 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, 3, 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: [18, 18, 18, 11, 11, 1, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 9, 9, 9, 9, 18, 18, 18] 46 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]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 699) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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]c3ccc(Br)cc32)nc(C)c1Br) `ZINC001184478462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184478462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001184478462 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc(C)c1Br 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.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'Br', '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, 1, 17, 1, 1, 8, 1, 5, 1, 17, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 11, 11, 1, 11, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 11, 9, 9, 9, 9, 18, 18, 18] 47 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]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184478462 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184478462 Building ZINC001184479770 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479770 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 700) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncccc1OCc1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479770 none O=C(Nc1ncccc1OCc1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 16, 29, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 29, 29, 30, 30, 30, 30, 30, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 701) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncccc1OCc1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479770 none O=C(Nc1ncccc1OCc1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 16, 29, 30, 30, 29, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 29, 29, 30, 30, 30, 30, 30, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479770 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 Building ZINC001184479770 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479770 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 700) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncccc1OCc1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479770 none O=C(Nc1ncccc1OCc1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 16, 29, 30, 30, 30, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 29, 29, 30, 30, 30, 30, 30, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 701) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncccc1OCc1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479770 none O=C(Nc1ncccc1OCc1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 16, 29, 30, 30, 29, 30, 30, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 29, 29, 30, 30, 30, 30, 30, 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]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479770 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479770 Building ZINC001184479530 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479530 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 702) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184479530 none O=C(Nc1ccnn1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 11, 11, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 703) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184479530 none O=C(Nc1ccnn1c1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 10, 10, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479530 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 Building ZINC001184479530 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479530 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 702) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479530.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184479530 none O=C(Nc1ccnn1c1cccc(Br)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 11, 11, 11, 11, 11, 17, 17, 17, 17, 17, 14, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 11, 11, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 703) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479530.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184479530 none O=C(Nc1ccnn1c1cccc(Br)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need 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, 10, 10, 10, 10, 10, 17, 17, 17, 17, 17, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 10, 10, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 17, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479530 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479530 Building ZINC001184479534 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479534 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 704) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n(c2cccnc2)n1) `ZINC001184479534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184479534 none CC(C)(C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 14, 12, 12, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 19, 19, 19, 19, 19, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 6, 8, 8, 8, 8, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 705) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n(c2cccnc2)n1) `ZINC001184479534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184479534 none CC(C)(C)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 14, 12, 12, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 19, 19, 19, 19, 19, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 6, 8, 8, 8, 8, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479534 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 Building ZINC001184479534 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479534 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 704) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n(c2cccnc2)n1) `ZINC001184479534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184479534 none CC(C)(C)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 14, 12, 12, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 19, 19, 19, 19, 19, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 6, 8, 8, 8, 8, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 705) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n(c2cccnc2)n1) `ZINC001184479534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184479534 none CC(C)(C)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)n(c2cccnc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 1, 1, 1, 8, 1, 8, 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, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 12, 14, 14, 12, 12, 6, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 12, 19, 19, 19, 19, 19, 12, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 6, 8, 8, 8, 8, 19, 19, 19, 19] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 62 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479534 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479534 Building ZINC001184479503 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479503 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 706) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2noc3ccc(F)cc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479503 none O=C(N1CCC(c2noc3ccc(F)cc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 30, 30, 30, 9, 9, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 707) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2noc3ccc(F)cc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479503 none O=C(N1CCC(c2noc3ccc(F)cc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 36, 36, 36, 14, 14, 14, 14, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479503 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 Building ZINC001184479503 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479503 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 706) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2noc3ccc(F)cc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479503 none O=C(N1CCC(c2noc3ccc(F)cc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 7, 9, 9, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 9, 9, 9, 9, 9, 30, 30, 30, 9, 9, 9, 9, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 707) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2noc3ccc(F)cc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479503 none O=C(N1CCC(c2noc3ccc(F)cc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.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', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 8, 12, 1, 1, 1, 1, 15, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 14, 14, 14, 36, 36, 36, 36, 36, 36, 36, 36, 36, 14, 14, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 14, 14, 14, 36, 36, 36, 14, 14, 14, 14, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479503 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479503 Building ZINC001184479553 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479553 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 708) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cncc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479553 none O=C(Nc1cncc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.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', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 15, 19, 19, 21, 21, 20, 21, 21, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 15, 15, 19, 19, 21, 21, 21, 21, 21, 15, 8, 8, 8, 8] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 709) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cncc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479553 none O=C(Nc1cncc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.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', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 14, 14, 19, 19, 21, 21, 20, 21, 21, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 14, 14, 19, 19, 21, 21, 21, 21, 21, 14, 8, 8, 8, 8] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479553 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 Building ZINC001184479553 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479553 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 708) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cncc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479553.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479553 none O=C(Nc1cncc(OCc2ccccc2)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.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', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 15, 15, 15, 15, 19, 19, 21, 21, 20, 21, 21, 15, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 15, 15, 19, 19, 21, 21, 21, 21, 21, 15, 8, 8, 8, 8] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 709) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cncc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479553.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184479553 none O=C(Nc1cncc(OCc2ccccc2)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.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', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 12, 5, 1, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 14, 14, 14, 14, 14, 19, 19, 21, 21, 20, 21, 21, 14, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 14, 14, 19, 19, 21, 21, 21, 21, 21, 14, 8, 8, 8, 8] 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479553 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479553 Building ZINC001184479573 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479573 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 710) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479573 none O=C(Nc1ccnn1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 14, 14, 14, 14, 29, 29, 26, 29, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 29, 29, 26, 29, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 711) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479573 none O=C(Nc1ccnn1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 28, 28, 28, 28, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479573 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 Building ZINC001184479573 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479573 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 710) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479573.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479573 none O=C(Nc1ccnn1c1ccccc1C(F)(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 14, 14, 14, 14, 29, 29, 26, 29, 29, 29, 29, 29, 29, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 29, 29, 26, 29, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 711) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccnn1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184479573.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184479573 none O=C(Nc1ccnn1c1ccccc1C(F)(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 14, 14, 14, 14, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 14, 14, 28, 28, 28, 28, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479573 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479573 Building ZINC001184479624 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479624 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 712) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2nc3c(c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CSC3)cc1) `ZINC001184479624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184479624 none COc1ccc(n2nc3c(c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CSC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 12, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 12, 7, 7, 7, 7, 19, 19, 19, 19, 21, 21] 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]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 713) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2nc3c(c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CSC3)cc1) `ZINC001184479624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184479624 none COc1ccc(n2nc3c(c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CSC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 11, 8, 8, 8, 8, 19, 19, 19, 19, 20, 20] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479624 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 Building ZINC001184479624 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184479624 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 712) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2nc3c(c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CSC3)cc1) `ZINC001184479624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184479624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184479624 none COc1ccc(n2nc3c(c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CSC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 19, 19, 19, 19, 19, 12, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 19, 19, 19, 21, 21, 21, 21, 21, 21, 21, 12, 7, 7, 7, 7, 19, 19, 19, 19, 21, 21] 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]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 713) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(n2nc3c(c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CSC3)cc1) `ZINC001184479624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184479624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001184479624 none COc1ccc(n2nc3c(c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)CSC3)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'S.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 8, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 14, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 19, 19, 19, 19, 11, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 11, 8, 8, 8, 8, 19, 19, 19, 19, 20, 20] 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]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184479624 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184479624 Building ZINC001184480112 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480112 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 714) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1noc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1c1ccccc1) `ZINC001184480112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480112 none CCOC(=O)c1noc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.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', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 8, 12, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 3, 12, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 3, 6, 6, 18, 18, 18, 18, 18, 3, 6, 6, 6, 6, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 715) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1noc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1c1ccccc1) `ZINC001184480112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480112 none CCOC(=O)c1noc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.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', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 8, 12, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 3, 6, 6, 6, 6, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480112 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 Building ZINC001184480112 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480112 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 714) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1noc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1c1ccccc1) `ZINC001184480112.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480112 none CCOC(=O)c1noc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.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', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 8, 12, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 3, 12, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 3, 6, 6, 18, 18, 18, 18, 18, 3, 6, 6, 6, 6, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 715) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1noc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1c1ccccc1) `ZINC001184480112.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184480112 none CCOC(=O)c1noc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.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', 'C.ar', 'Br', 'C.ar', 'C.ar', '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, 8, 12, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 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, 3, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 11, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 3, 6, 6, 6, 6, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480112 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480112 Building ZINC001184480199 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480199 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 716) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(COC[C@@]23CCC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)C3)c1) `ZINC001184480199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480199 none Cc1cncc(COC[C@@]23CCC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)C3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 25, 11, 8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 41, 41, 41, 41, 41, 41, 25, 25, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 41] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 717) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(COC[C@@]23CCC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)C3)c1) `ZINC001184480199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480199 none Cc1cncc(COC[C@@]23CCC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)C3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 6, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 42, 42, 42, 42, 42, 42, 26, 26, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 42] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480199 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 Building ZINC001184480199 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480199 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 716) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(COC[C@@]23CCC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)C3)c1) `ZINC001184480199.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480199 none Cc1cncc(COC[C@@]23CCC[C@@H]2CN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)C3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 25, 11, 8, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 41, 41, 41, 41, 41, 41, 25, 25, 8, 8, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 4, 4, 41] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 717) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cncc(COC[C@@]23CCC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)C3)c1) `ZINC001184480199.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480199 none Cc1cncc(COC[C@@]23CCC[C@@H]2CN(C(=O)[C@]([O-])([SiH3])c2c[nH]c4ccc(Br)cc42)C3)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 14, 6, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 42, 42, 42, 42, 42, 42, 26, 26, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 42] 50 rigid atoms, others: [16, 17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480199 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480199 Building ZINC001184480211 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480211 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 718) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cncc(Br)c1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001184480211 none O=C(Nc1cncc(Br)c1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 17, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 719) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cncc(Br)c1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001184480211 none O=C(Nc1cncc(Br)c1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 17, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 27, 27, 9, 9, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480211 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 Building ZINC001184480211 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480211 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 718) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cncc(Br)c1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001184480211 none O=C(Nc1cncc(Br)c1Cl)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 17, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 28, 28, 9, 9, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 719) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cncc(Br)c1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 34 natoms 33 natoms 32 natoms 31 names: ZINC001184480211 none O=C(Nc1cncc(Br)c1Cl)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'Cl', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 8, 1, 1, 17, 1, 16, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 7, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 27, 27, 9, 9, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480211 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480211 Building ZINC001184480227 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480227 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 720) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(c3ccccc3F)nn2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480227 none O=C(Nc1ccc2nc(c3ccccc3F)nn2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'N.pl3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 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, 12, 12, 12, 12, 34, 34, 19, 34, 34, 34, 12, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 34, 34, 34, 34, 12, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 721) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(c3ccccc3F)nn2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480227 none O=C(Nc1ccc2nc(c3ccccc3F)nn2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'N.pl3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 11, 32, 32, 19, 32, 32, 32, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 32, 32, 32, 32, 11, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480227 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 Building ZINC001184480227 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480227 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 720) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(c3ccccc3F)nn2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480227 none O=C(Nc1ccc2nc(c3ccccc3F)nn2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'N.pl3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 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, 12, 12, 12, 12, 34, 34, 19, 34, 34, 34, 12, 12, 12, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 34, 34, 34, 34, 12, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 721) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2nc(c3ccccc3F)nn2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480227 none O=C(Nc1ccc2nc(c3ccccc3F)nn2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.2', 'N.pl3', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 8, 8, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 11, 32, 32, 19, 32, 32, 32, 11, 11, 11, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 11, 11, 32, 32, 32, 32, 11, 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]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480227 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480227 Building ZINC001184480532 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480532 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/722 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/722' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/723 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/723' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 724) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 725) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480532 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 Building ZINC001184480532 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480532 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 722) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 28, 28, 28, 28, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 723) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 28, 28, 28, 28, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 724) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 725) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480532 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 Building ZINC001184480532 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480532 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 722) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 28, 28, 28, 28, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 723) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 28, 28, 28, 28, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 724) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 725) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480532 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 Building ZINC001184480532 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480532 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 722) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 28, 28, 28, 28, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 723) grep: /scratch/xiaobo/281161/xco-8058088.67/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: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 14, 28, 28, 28, 28, 28, 28, 7, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 28, 28, 28, 28, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 724) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 725) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480532.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480532 none O=C(N1CCC[C@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 13, 30, 30, 30, 30, 30, 30, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 13, 13, 30, 30, 30, 30, 6, 6, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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/281161/xco-8058088.67/working/building/ZINC001184480532 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480532 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480532 Building ZINC001184480534 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480534 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/726 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/727 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/727' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 728) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 729) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480534 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 Building ZINC001184480534 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480534 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 726) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 24, 24, 24, 24, 6, 6, 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, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 727) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 24, 24, 24, 24, 6, 6, 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, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 728) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 729) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480534 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 Building ZINC001184480534 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480534 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 726) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 24, 24, 24, 24, 6, 6, 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, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 727) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 24, 24, 24, 24, 6, 6, 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, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 728) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 729) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480534 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 Building ZINC001184480534 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184480534 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 726) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/726: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 24, 24, 24, 24, 6, 6, 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, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 727) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/727: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 6, 6, 6, 6, 6, 6, 6, 14, 24, 24, 24, 24, 24, 24, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 14, 14, 24, 24, 24, 24, 6, 6, 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, 53]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 728) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 729) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480534.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184480534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480534 none O=C(N1CCC[C@@]2(CCN2Cc2cccc(F)c2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 4, 5, 5, 5, 5, 5, 5, 5, 5, 13, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 13, 13, 28, 28, 28, 28, 5, 5, 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, 53]) total number of confs: 80 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480534 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480534 Building ZINC001184480558 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480558 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 730) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)n1) `ZINC001184480558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001184480558 none Cc1cc(C)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 731) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)n1) `ZINC001184480558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001184480558 none Cc1cc(C)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 8, 8, 8, 8] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480558 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 Building ZINC001184480558 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480558 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 730) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)n1) `ZINC001184480558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001184480558 none Cc1cc(C)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 1, 6, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 9, 9, 9, 9] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 731) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(C)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)n1) `ZINC001184480558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 40 natoms 39 natoms 38 natoms 37 names: ZINC001184480558 none Cc1cc(C)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c(Br)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 17, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 6, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 6, 8, 8, 8, 8] 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480558 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480558 Building ZINC001184480593 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480593 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 732) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc(C)nc(SC)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184480593 none CSc1cc(C)nc(SC)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'S.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 5, 8, 1, 14, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [16, 9, 9, 9, 9, 9, 9, 9, 9, 26, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 9, 9, 9, 9, 26, 26, 26, 2, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 733) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc(C)nc(SC)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184480593 none CSc1cc(C)nc(SC)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'S.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 5, 8, 1, 14, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [17, 9, 9, 9, 9, 9, 9, 9, 9, 26, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 9, 9, 9, 9, 26, 26, 26, 2, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480593 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 Building ZINC001184480593 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480593 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 732) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc(C)nc(SC)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480593.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184480593 none CSc1cc(C)nc(SC)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'S.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 5, 8, 1, 14, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [16, 9, 9, 9, 9, 9, 9, 9, 9, 26, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 9, 9, 9, 9, 26, 26, 26, 2, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 733) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CSc1cc(C)nc(SC)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480593.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184480593 none CSc1cc(C)nc(SC)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'S.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 1, 1, 1, 5, 8, 1, 14, 5, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 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: [17, 9, 9, 9, 9, 9, 9, 9, 9, 26, 2, 2, 1, 2, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 9, 9, 9, 9, 26, 26, 26, 2, 6, 6, 6, 6] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480593 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480593 Building ZINC001184480611 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480611 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 734) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184480611 none CN(C(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 11, 21, 26, 26, 27, 27, 27, 27, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 22, 22, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 4, 4, 4, 4, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 735) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184480611 none CN(C(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 11, 22, 27, 27, 27, 27, 27, 27, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 23, 23, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 4, 4, 4, 4, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480611 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 Building ZINC001184480611 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480611 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 734) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184480611 none CN(C(=O)OC(C)(C)C)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 11, 21, 26, 26, 27, 27, 27, 27, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 22, 22, 22, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 4, 4, 4, 4, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 735) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1) `ZINC001184480611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001184480611 none CN(C(=O)OC(C)(C)C)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cn1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 8, 1, 11, 12, 5, 5, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [23, 11, 22, 27, 27, 27, 27, 27, 27, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 23, 23, 23, 27, 27, 27, 27, 27, 27, 27, 27, 27, 11, 11, 3, 4, 4, 4, 4, 11] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480611 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480611 Building ZINC001184480628 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480628 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 736) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Br)cc1OC(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184480628 none O=C(Nc1ncc(Br)cc1OC(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 17, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 13, 13, 24, 29, 29, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 29, 7, 7, 7, 7] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 737) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Br)cc1OC(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184480628 none O=C(Nc1ncc(Br)cc1OC(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 17, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 13, 13, 24, 29, 29, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 29, 7, 7, 7, 7] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480628 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 Building ZINC001184480628 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480628 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 736) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Br)cc1OC(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184480628 none O=C(Nc1ncc(Br)cc1OC(F)F)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 17, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 13, 13, 24, 29, 29, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 29, 7, 7, 7, 7] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 737) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ncc(Br)cc1OC(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184480628 none O=C(Nc1ncc(Br)cc1OC(F)F)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 8, 1, 1, 17, 1, 1, 12, 5, 15, 15, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 13, 13, 13, 13, 13, 13, 24, 29, 29, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 13, 13, 29, 7, 7, 7, 7] 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: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480628 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480628 Building ZINC001184480885 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480885 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 738) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C[C@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480885 none O=C(N1CCC[C@@]2(C[C@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 15, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 24, 26, 26, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 26, 26, 26, 24, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 739) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C[C@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480885 none O=C(N1CCC[C@@]2(C[C@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 19, 20, 20, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 19, 19, 19, 19, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 43 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480885 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 Building ZINC001184480885 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480885 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 738) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C[C@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480885.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480885 none O=C(N1CCC[C@@]2(C[C@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 15, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 24, 26, 26, 24, 24, 24, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 26, 26, 26, 24, 24, 24, 24, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 739) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C[C@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480885.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480885 none O=C(N1CCC[C@@]2(C[C@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 19, 20, 20, 19, 19, 19, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 20, 20, 20, 20, 20, 19, 19, 19, 19, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 43 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480885 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480885 Building ZINC001184480886 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480886 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 740) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C[C@@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480886 none O=C(N1CCC[C@@]2(C[C@@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 12, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 20, 25, 25, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 20, 25, 25, 20, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 741) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C[C@@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480886 none O=C(N1CCC[C@@]2(C[C@@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 19, 19, 23, 23, 19, 23, 23, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 23, 23, 19, 23, 23, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480886 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 Building ZINC001184480886 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480886 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 740) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C[C@@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480886.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480886 none O=C(N1CCC[C@@]2(C[C@@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 12, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 20, 25, 25, 20, 20, 20, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 25, 25, 20, 25, 25, 20, 20, 20, 20, 5, 5, 5, 5] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 741) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@@]2(C[C@@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480886.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480886 none O=C(N1CCC[C@@]2(C[C@@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 19, 19, 19, 19, 19, 19, 19, 19, 23, 23, 19, 23, 23, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 23, 23, 19, 23, 23, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480886 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480886 Building ZINC001184480887 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480887 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 742) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C[C@@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480887 none O=C(N1CCC[C@]2(C[C@@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 743) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C[C@@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480887 none O=C(N1CCC[C@]2(C[C@@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 10, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 20, 22, 22, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 20, 22, 22, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480887 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 Building ZINC001184480887 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480887 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 742) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C[C@@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480887.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480887 none O=C(N1CCC[C@]2(C[C@@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 42 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 743) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C[C@@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480887.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480887 none O=C(N1CCC[C@]2(C[C@@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need 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, 10, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 20, 22, 22, 20, 20, 20, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20, 22, 22, 20, 22, 22, 20, 20, 20, 20, 6, 6, 6, 6] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480887 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480887 Building ZINC001184480888 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480888 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 744) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C[C@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480888 none O=C(N1CCC[C@]2(C[C@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 19, 21, 21, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 21, 21, 21, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 745) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C[C@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480888 none O=C(N1CCC[C@]2(C[C@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 13, 18, 18, 18, 18, 18, 18, 18, 18, 23, 23, 20, 23, 23, 18, 18, 18, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 23, 23, 23, 23, 23, 18, 18, 18, 18, 7, 7, 7, 7] 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]) total number of confs: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480888 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 Building ZINC001184480888 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184480888 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 744) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C[C@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480888.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184480888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480888 none O=C(N1CCC[C@]2(C[C@H](c3ccccc3)CO2)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 2, 12, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 19, 21, 21, 19, 19, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 21, 21, 21, 21, 21, 19, 19, 19, 19, 6, 6, 6, 6] 50 rigid atoms, others: [19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 57 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 745) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC[C@]2(C[C@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184480888.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184480888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184480888 none O=C(N1CCC[C@]2(C[C@H](c3ccccc3)CO2)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 12, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [9, 2, 13, 18, 18, 18, 18, 18, 18, 18, 18, 23, 23, 20, 23, 23, 18, 18, 18, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 23, 23, 23, 23, 23, 18, 18, 18, 18, 7, 7, 7, 7] 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]) total number of confs: 66 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184480888 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184480888 Building ZINC001184481187 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481187 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 746) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2ncn3cc(c4ccoc4)ccc23)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184481187 none O=C(N1CC(c2ncn3cc(c4ccoc4)ccc23)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 34, 34, 34, 34, 15, 15, 15, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 34, 34, 34, 15, 15, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 20, 21, 22] set([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]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 747) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2ncn3cc(c4ccoc4)ccc23)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184481187 none O=C(N1CC(c2ncn3cc(c4ccoc4)ccc23)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 19, 38, 38, 38, 38, 19, 19, 19, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 38, 38, 38, 19, 19, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 20, 21, 22] set([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]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481187 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 Building ZINC001184481187 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481187 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 746) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2ncn3cc(c4ccoc4)ccc23)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481187.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184481187 none O=C(N1CC(c2ncn3cc(c4ccoc4)ccc23)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 34, 34, 34, 34, 15, 15, 15, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 15, 15, 34, 34, 34, 15, 15, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 20, 21, 22] set([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]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 747) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(c2ncn3cc(c4ccoc4)ccc23)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481187.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001184481187 none O=C(N1CC(c2ncn3cc(c4ccoc4)ccc23)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 8, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 3, 19, 19, 19, 19, 19, 19, 38, 38, 38, 38, 19, 19, 19, 3, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 19, 19, 38, 38, 38, 19, 19, 3, 3, 3, 3, 3, 3] 50 rigid atoms, others: [0, 1, 2, 20, 21, 22] set([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]) total number of confs: 60 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481187 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481187 Building ZINC001184481192 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481192 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 748) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184481192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481192 none CC(C)(C)OC(=O)N1CCC[C@@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 13, 21, 13, 13, 13, 13, 13, 13, 13, 13, 4, 3, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 749) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184481192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481192 none CC(C)(C)OC(=O)N1CCC[C@@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 28, 28, 20, 14, 20, 14, 14, 14, 14, 14, 14, 14, 14, 7, 3, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481192 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 Building ZINC001184481192 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481192 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 748) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184481192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481192 none CC(C)(C)OC(=O)N1CCC[C@@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 13, 21, 13, 13, 13, 13, 13, 13, 13, 13, 4, 3, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 13, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 4, 4, 13, 13] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 749) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184481192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481192 none CC(C)(C)OC(=O)N1CCC[C@@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 28, 28, 20, 14, 20, 14, 14, 14, 14, 14, 14, 14, 14, 7, 3, 10, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 28, 28, 28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14] 50 rigid atoms, others: [18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481192 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481192 Building ZINC001184481195 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481195 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 750) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184481195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481195 none CC(C)(C)OC(=O)N1CCC[C@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 7, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 751) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184481195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481195 none CC(C)(C)OC(=O)N1CCC[C@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 22, 22, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481195 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 Building ZINC001184481195 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481195 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 750) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184481195.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481195 none CC(C)(C)OC(=O)N1CCC[C@]2(CCCN2C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 7, 2, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 751) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1) `ZINC001184481195.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481195 none CC(C)(C)OC(=O)N1CCC[C@]2(CCCN2C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 22, 22, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 6, 2, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 22, 22, 22, 22, 22, 22, 22, 22, 22, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 6, 6] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481195 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481195 Building ZINC001184481219 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481219 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 752) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184481219 none Cc1nnc(C(C)C)n1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8] 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: 41 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 753) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184481219 none Cc1nnc(C(C)C)n1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 40 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481219 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 Building ZINC001184481219 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481219 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 752) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481219.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184481219 none Cc1nnc(C(C)C)n1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8] 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: 41 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 753) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481219.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001184481219 none Cc1nnc(C(C)C)n1C1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 7, 7] 50 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 40 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481219 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481219 Building ZINC001184481221 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481221 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 754) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481221 none CC(C)(C)OC(=O)N1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 21, 14, 14, 14, 14, 14, 14, 14, 8, 2, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14, 14, 14] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 755) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481221 none CC(C)(C)OC(=O)N1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 15, 24, 15, 15, 15, 15, 15, 15, 15, 5, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 15, 15, 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, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481221 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 Building ZINC001184481221 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481221 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 754) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481221.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481221 none CC(C)(C)OC(=O)N1CCCC12CCN(C(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 14, 21, 14, 14, 14, 14, 14, 14, 14, 8, 2, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 14, 14, 14, 14] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 755) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)CC2) `ZINC001184481221.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184481221 none CC(C)(C)OC(=O)N1CCCC12CCN(C(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 15, 24, 15, 15, 15, 15, 15, 15, 15, 5, 2, 9, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 28, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 5, 15, 15, 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, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481221 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481221 Building ZINC001184481264 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481264 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 756) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccc(F)cc2Cl)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481264 none O=C(N1CCC(Oc2ccc(F)cc2Cl)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 25, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 757) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccc(F)cc2Cl)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481264 none O=C(N1CCC(Oc2ccc(F)cc2Cl)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 28, 28, 28, 28, 28, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481264 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 Building ZINC001184481264 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481264 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 756) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccc(F)cc2Cl)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481264 none O=C(N1CCC(Oc2ccc(F)cc2Cl)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 25, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 25, 25, 25, 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]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 757) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccc(F)cc2Cl)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184481264 none O=C(N1CCC(Oc2ccc(F)cc2Cl)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 12, 1, 1, 1, 1, 15, 1, 1, 16, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 15, 28, 28, 28, 28, 28, 28, 28, 4, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 28, 28, 28, 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]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481264 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481264 Building ZINC001184481611 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481611 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 758) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1NC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481611 none Cc1cccc(C)c1NC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 24, 25, 25, 25, 24, 24, 7, 24, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 24, 25, 25, 25, 25, 24, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 759) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1NC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481611 none Cc1cccc(C)c1NC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 22, 23, 23, 23, 22, 22, 9, 22, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 22, 23, 23, 23, 23, 22, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481611 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 Building ZINC001184481611 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481611 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 758) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1NC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481611.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481611 none Cc1cccc(C)c1NC(=O)[C@@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 24, 25, 25, 25, 24, 24, 7, 24, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 25, 25, 24, 25, 25, 25, 25, 24, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 71 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 759) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1NC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481611.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481611 none Cc1cccc(C)c1NC(=O)[C@@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 22, 23, 23, 23, 22, 22, 9, 22, 9, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 23, 22, 23, 23, 23, 23, 22, 9, 9, 9, 9, 9, 9, 9, 9, 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]) total number of confs: 71 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481611 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481611 Building ZINC001184481612 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481612 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 760) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1NC(=O)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481612 none Cc1cccc(C)c1NC(=O)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 18, 20, 20, 20, 18, 18, 8, 18, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 18, 20, 20, 20, 20, 18, 8, 8, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 67 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 761) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1NC(=O)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481612 none Cc1cccc(C)c1NC(=O)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 19, 22, 22, 22, 19, 19, 7, 19, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 19, 22, 22, 22, 22, 19, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481612 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 Building ZINC001184481612 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184481612 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 760) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1NC(=O)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184481612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481612 none Cc1cccc(C)c1NC(=O)[C@H]1CCCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 18, 20, 20, 20, 18, 18, 8, 18, 8, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 20, 20, 18, 20, 20, 20, 20, 18, 8, 8, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 67 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 761) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1NC(=O)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184481612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184481612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001184481612 none Cc1cccc(C)c1NC(=O)[C@H]1CCCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'N.am', 'C.2', 'O.2', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 5, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 19, 22, 22, 22, 19, 19, 7, 19, 7, 7, 7, 7, 7, 7, 6, 1, 6, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 22, 22, 19, 22, 22, 22, 22, 19, 7, 7, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 69 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184481612 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184481612 Building ZINC001184484281 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484281 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 762) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1coc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)n1) `ZINC001184484281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484281 none CCOC(=O)c1coc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 26, 23, 26, 23, 23, 23, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 23, 32, 32, 32, 32, 32, 23, 12, 12, 12, 3, 4, 4, 4, 4, 12] 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 763) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1coc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)n1) `ZINC001184484281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484281 none CCOC(=O)c1coc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 24, 27, 24, 24, 24, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 24, 32, 32, 32, 32, 32, 24, 12, 12, 12, 3, 4, 4, 4, 4, 12] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484281 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 Building ZINC001184484281 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484281 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 762) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1coc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)n1) `ZINC001184484281.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484281 none CCOC(=O)c1coc(c2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 26, 26, 23, 26, 23, 23, 23, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 23, 32, 32, 32, 32, 32, 23, 12, 12, 12, 3, 4, 4, 4, 4, 12] 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: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 763) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1coc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)n1) `ZINC001184484281.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484281 none CCOC(=O)c1coc(c2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.2', '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, 12, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 24, 27, 24, 24, 24, 12, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 24, 32, 32, 32, 32, 32, 24, 12, 12, 12, 3, 4, 4, 4, 4, 12] 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: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484281 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484281 Building ZINC001184484282 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484282 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 764) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Br)c[nH]c21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184484282 none O=C(Nc1cccc2c(Br)c[nH]c21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Br', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 6, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 20, 20, 20, 20, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 765) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Br)c[nH]c21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184484282 none O=C(Nc1cccc2c(Br)c[nH]c21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Br', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 6, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 20, 20, 20, 20, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484282 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 Building ZINC001184484282 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484282 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 764) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Br)c[nH]c21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184484282 none O=C(Nc1cccc2c(Br)c[nH]c21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Br', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 6, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 20, 20, 20, 20, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 765) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cccc2c(Br)c[nH]c21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184484282 none O=C(Nc1cccc2c(Br)c[nH]c21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'Br', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 1, 17, 1, 8, 6, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 20, 20, 20, 20, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484282 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484282 Building ZINC001184484295 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484295 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 766) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)c1) `ZINC001184484295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484295 none CNC(=O)c1cccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 24, 11, 4, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 3, 4, 4, 4, 4, 12, 12, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 767) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)c1) `ZINC001184484295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484295 none CNC(=O)c1cccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 24, 12, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 3, 4, 4, 4, 4, 12, 12, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484295 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 Building ZINC001184484295 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484295 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 766) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)c1) `ZINC001184484295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484295 none CNC(=O)c1cccc(Oc2ccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 24, 11, 4, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 3, 4, 4, 4, 4, 12, 12, 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 767) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)c1) `ZINC001184484295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484295 none CNC(=O)c1cccc(Oc2ccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)cc2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 24, 12, 6, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 27, 27, 27, 27, 27, 27, 27, 27, 12, 12, 3, 4, 4, 4, 4, 12, 12, 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]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484295 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484295 Building ZINC001184484410 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484410 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 768) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1(c2cccc(C(F)(F)F)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484410 none NC1(c2cccc(C(F)(F)F)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 21, 21, 11, 21, 21, 21, 21, 21, 21, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 21, 21, 20, 21, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 769) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1(c2cccc(C(F)(F)F)c2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484410 none NC1(c2cccc(C(F)(F)F)c2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 21, 21, 11, 21, 21, 21, 21, 21, 21, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 21, 21, 18, 21, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484410 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 Building ZINC001184484410 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484410 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 768) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1(c2cccc(C(F)(F)F)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484410 none NC1(c2cccc(C(F)(F)F)c2)CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 21, 21, 11, 21, 21, 21, 21, 21, 21, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 21, 21, 20, 21, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 74 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 769) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC1(c2cccc(C(F)(F)F)c2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484410 none NC1(c2cccc(C(F)(F)F)c2)CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 21, 21, 11, 21, 21, 21, 21, 21, 21, 6, 6, 4, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 21, 21, 18, 21, 6, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 70 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484410 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484410 Building ZINC001184484453 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484453 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 770) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1cc(Br)ccc1N) `ZINC001184484453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184484453 none CC(C)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1cc(Br)ccc1N 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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 17, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 17, 17, 17, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 771) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1cc(Br)ccc1N) `ZINC001184484453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184484453 none CC(C)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1cc(Br)ccc1N 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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 17, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 8, 18, 18, 18, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484453 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 Building ZINC001184484453 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484453 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 770) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1cc(Br)ccc1N) `ZINC001184484453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184484453 none CC(C)N(C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1cc(Br)ccc1N 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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 17, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 17, 17, 17, 8, 17, 17, 17, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 17, 17, 17, 17, 17] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 771) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1cc(Br)ccc1N) `ZINC001184484453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC001184484453 none CC(C)N(C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21)c1cc(Br)ccc1N 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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', '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, 1, 17, 1, 1, 1, 1, 1, 17, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 8, 18, 18, 18, 15, 15, 15, 15, 15, 15, 15, 8, 8, 8, 8, 18, 18, 18, 18, 18] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484453 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484453 Building ZINC001184484468 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484468 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 772) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F) `ZINC001184484468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001184484468 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 29, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 3, 5, 5, 5, 5, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 773) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F) `ZINC001184484468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001184484468 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 5, 29, 5, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 3, 5, 5, 5, 5, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484468 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 Building ZINC001184484468 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484468 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 772) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F) `ZINC001184484468.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001184484468 none COC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 3, 29, 3, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 3, 5, 5, 5, 5, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 773) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F) `ZINC001184484468.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 44 natoms 43 natoms 42 natoms 41 names: ZINC001184484468 none COC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1C(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 5, 15, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 5, 29, 5, 16, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 16, 16, 16, 29, 29, 29, 16, 16, 3, 5, 5, 5, 5, 16] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484468 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484468 Building ZINC001184484499 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484499 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 774) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]nc(c3ccncc3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184484499 none O=C(Nc1ccc2[nH]nc(c3ccncc3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 11, 24, 24, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 24, 24, 24, 24, 11, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 775) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]nc(c3ccncc3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184484499 none O=C(Nc1ccc2[nH]nc(c3ccncc3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 25, 25, 25, 25, 11, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484499 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 Building ZINC001184484499 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484499 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 774) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]nc(c3ccncc3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484499.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184484499 none O=C(Nc1ccc2[nH]nc(c3ccncc3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 24, 24, 11, 24, 24, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 24, 24, 24, 24, 11, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 775) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2[nH]nc(c3ccncc3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484499.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184484499 none O=C(Nc1ccc2[nH]nc(c3ccncc3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 6, 8, 1, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 25, 25, 25, 25, 25, 11, 11, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 11, 11, 25, 25, 25, 25, 11, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484499 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484499 Building ZINC001184484517 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484517 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/776 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 11, 5, 5, 5, 5, 5, 5, 5, 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, 16, 16, 5, 5, 5, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/777 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/777' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 23, 31, 11, 5, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 5, 5, 5, 3, 4, 4, 4, 4, 31, 31, 31, 31] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 778) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 11, 5, 5, 5, 5, 5, 5, 5, 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, 16, 16, 5, 5, 5, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 779) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 23, 31, 11, 5, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 5, 5, 5, 3, 4, 4, 4, 4, 31, 31, 31, 31] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484517 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 Building ZINC001184484517 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484517 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 776) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 33, 12, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 5, 5, 5, 3, 4, 4, 4, 4, 33, 33, 33, 33] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 777) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 24, 33, 12, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 18, 5, 5, 5, 3, 4, 4, 4, 4, 33, 33, 33, 33] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 778) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 11, 5, 5, 5, 5, 5, 5, 5, 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, 16, 16, 5, 5, 5, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 779) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 23, 31, 11, 5, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 5, 5, 5, 3, 4, 4, 4, 4, 31, 31, 31, 31] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484517 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 Building ZINC001184484517 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484517 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 776) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 33, 12, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 5, 5, 5, 3, 4, 4, 4, 4, 33, 33, 33, 33] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 777) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 24, 33, 12, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 18, 5, 5, 5, 3, 4, 4, 4, 4, 33, 33, 33, 33] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 778) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 11, 5, 5, 5, 5, 5, 5, 5, 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, 16, 16, 5, 5, 5, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 779) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 23, 31, 11, 5, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 5, 5, 5, 3, 4, 4, 4, 4, 31, 31, 31, 31] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484517 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 Building ZINC001184484517 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484517 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 776) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/776: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 33, 12, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 17, 17, 5, 5, 5, 3, 4, 4, 4, 4, 33, 33, 33, 33] 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: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 777) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/777: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 24, 33, 12, 5, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33, 33, 33, 18, 18, 5, 5, 5, 3, 4, 4, 4, 4, 33, 33, 33, 33] 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: 96 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 778) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@H](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 11, 5, 5, 5, 5, 5, 5, 5, 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, 16, 16, 5, 5, 5, 3, 4, 4, 4, 4, 30, 30, 30, 30] 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: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 779) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484517.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484517 none C[N@]1CC[C@@H](COc2cccc(F)c2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.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, 10, 5, 5, 5, 7, 5, 12, 1, 1, 1, 1, 1, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 23, 31, 11, 5, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 18, 18, 5, 5, 5, 3, 4, 4, 4, 4, 31, 31, 31, 31] 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: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484517 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484517 Building ZINC001184484554 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484554 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/780 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/781 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/781' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 782) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 783) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484554 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 Building ZINC001184484554 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484554 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 780) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 24, 24, 24, 24, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 24, 24, 24, 24, 24, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 781) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 24, 24, 24, 24, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 24, 24, 24, 24, 24, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 782) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 783) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484554 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 Building ZINC001184484554 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484554 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 780) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 24, 24, 24, 24, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 24, 24, 24, 24, 24, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 781) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 24, 24, 24, 24, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 24, 24, 24, 24, 24, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 782) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 783) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484554 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 Building ZINC001184484554 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484554 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 780) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/780: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 24, 24, 24, 24, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 24, 24, 24, 24, 24, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 781) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 24, 24, 24, 24, 24, 11, 11, 5, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 21, 21, 24, 24, 24, 24, 24, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 782) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 783) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484554.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484554 none CC1(C)CN(Cc2ccccc2)CC[C@@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 28, 28, 25, 28, 28, 11, 11, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 22, 22, 28, 28, 25, 28, 28, 11, 11, 11, 11, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484554 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484554 Building ZINC001184484555 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484555 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/784 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/785 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/785' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 786) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 787) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484555 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 Building ZINC001184484555 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484555 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 784) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 29, 26, 29, 29, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 29, 29, 26, 29, 29, 12, 12, 12, 12, 3, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 785) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 29, 26, 29, 29, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 29, 29, 26, 29, 29, 12, 12, 12, 12, 3, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 786) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 787) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484555 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 Building ZINC001184484555 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484555 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 784) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 29, 26, 29, 29, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 29, 29, 26, 29, 29, 12, 12, 12, 12, 3, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 785) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 29, 26, 29, 29, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 29, 29, 26, 29, 29, 12, 12, 12, 12, 3, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 786) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 787) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484555 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 Building ZINC001184484555 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184484555 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 784) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/784: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 29, 26, 29, 29, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 29, 29, 26, 29, 29, 12, 12, 12, 12, 3, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 785) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 29, 29, 26, 29, 29, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 24, 24, 29, 29, 26, 29, 29, 12, 12, 12, 12, 3, 5, 5, 5, 5] 50 rigid atoms, others: [17, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 786) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 787) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484555.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184484555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001184484555 none CC1(C)CN(Cc2ccccc2)CC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 25, 25, 22, 25, 25, 12, 12, 6, 12, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 22, 22, 25, 25, 22, 25, 25, 12, 12, 12, 12, 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, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484555 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484555 Building ZINC001184484619 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484619 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 788) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(Cc2ccccc2F)C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484619 none N[C@H]1CC[C@H](N(Cc2ccccc2F)C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 6, 11, 3, 6, 13, 19, 19, 17, 19, 19, 19, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 19, 19, 19, 19, 5, 5, 5, 5, 11, 11, 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]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 789) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(Cc2ccccc2F)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484619 none N[C@H]1CC[C@H](N(Cc2ccccc2F)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 6, 11, 3, 6, 12, 19, 19, 12, 19, 19, 19, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 19, 19, 19, 19, 5, 5, 5, 5, 11, 11, 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]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484619 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 Building ZINC001184484619 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484619 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 788) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(Cc2ccccc2F)C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484619 none N[C@H]1CC[C@H](N(Cc2ccccc2F)C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 6, 11, 3, 6, 13, 19, 19, 17, 19, 19, 19, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 13, 13, 19, 19, 19, 19, 5, 5, 5, 5, 11, 11, 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]) total number of confs: 91 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 789) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(Cc2ccccc2F)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184484619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184484619 none N[C@H]1CC[C@H](N(Cc2ccccc2F)C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 5, 1, 1, 1, 1, 1, 1, 15, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 6, 11, 3, 6, 12, 19, 19, 12, 19, 19, 19, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 19, 19, 19, 19, 5, 5, 5, 5, 11, 11, 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]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484619 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484619 Building ZINC001184484737 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484737 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 790) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C2(C(F)(F)F)N=N2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484737 none O=C(NCc1ccc(C2(C(F)(F)F)N=N2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 5, 15, 15, 15, 8, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 21, 21, 12, 12, 34, 34, 34, 34, 34, 34, 21, 21, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 21, 21, 21, 21, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 791) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C2(C(F)(F)F)N=N2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484737 none O=C(NCc1ccc(C2(C(F)(F)F)N=N2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 5, 15, 15, 15, 8, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 21, 21, 15, 17, 34, 34, 34, 34, 34, 34, 21, 21, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 21, 21, 21, 21, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484737 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 Building ZINC001184484737 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484737 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 790) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C2(C(F)(F)F)N=N2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484737.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484737 none O=C(NCc1ccc(C2(C(F)(F)F)N=N2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 5, 15, 15, 15, 8, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 21, 21, 12, 12, 34, 34, 34, 34, 34, 34, 21, 21, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 21, 21, 21, 21, 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]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 791) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(C2(C(F)(F)F)N=N2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484737.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184484737 none O=C(NCc1ccc(C2(C(F)(F)F)N=N2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'F', 'F', 'F', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 5, 5, 15, 15, 15, 8, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 21, 21, 15, 17, 34, 34, 34, 34, 34, 34, 21, 21, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 12, 12, 21, 21, 21, 21, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484737 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484737 Building ZINC001184484745 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484745 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 792) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccccc2C(F)(F)F)CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184484745 none O=C(NC1(c2ccccc2C(F)(F)F)CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 56 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 793) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccccc2C(F)(F)F)CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184484745 none O=C(NC1(c2ccccc2C(F)(F)F)CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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: 58 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484745 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 Building ZINC001184484745 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484745 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 792) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccccc2C(F)(F)F)CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484745.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184484745 none O=C(NC1(c2ccccc2C(F)(F)F)CCOCC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 13, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 8, 8] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 56 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 793) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC1(c2ccccc2C(F)(F)F)CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184484745.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184484745 none O=C(NC1(c2ccccc2C(F)(F)F)CCOCC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need 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, 12, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 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: 58 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484745 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484745 Building ZINC001184484895 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484895 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 794) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1F) `ZINC001184484895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484895 none CC(C)(C)OC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 31, 11, 31, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 795) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1F) `ZINC001184484895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484895 none CC(C)(C)OC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 31, 11, 31, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484895 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895 Building ZINC001184484895 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184484895 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 794) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1F) `ZINC001184484895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184484895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484895 none CC(C)(C)OC(=O)c1cc(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 31, 11, 31, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 795) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1F) `ZINC001184484895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184484895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001184484895 none CC(C)(C)OC(=O)c1cc(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)ccc1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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] 0 hydrogens 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, 31, 11, 31, 11, 11, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11, 3, 4, 4, 4, 4, 11, 11] 50 rigid atoms, others: [11, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184484895 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184484895 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184484895 Building ZINC001184485229 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485229 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 796) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc1) `ZINC001184485229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184485229 none COc1ccc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc1 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', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 22, 22, 22, 20, 20, 11, 11, 11, 11, 4, 8, 8, 8, 8, 20] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 797) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc1) `ZINC001184485229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184485229 none COc1ccc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc1 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', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 20, 20, 20, 11, 11, 11, 9, 11, 11, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 22, 22, 22, 20, 20, 11, 11, 11, 11, 4, 8, 8, 8, 8, 20] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485229 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 Building ZINC001184485229 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485229 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 796) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc1) `ZINC001184485229.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184485229 none COc1ccc(c2ccccc2NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc1 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', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 20, 20, 20, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 22, 22, 22, 20, 20, 11, 11, 11, 11, 4, 8, 8, 8, 8, 20] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 797) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc1) `ZINC001184485229.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001184485229 none COc1ccc(c2ccccc2NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)nc1 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', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 20, 20, 20, 20, 11, 11, 11, 9, 11, 11, 4, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 22, 22, 22, 20, 20, 11, 11, 11, 11, 4, 8, 8, 8, 8, 20] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485229 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485229 Building ZINC001184485122 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485122 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 798) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CC1CCOCC1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184485122 none O=C(N[C@@H](CC1CCOCC1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 13, 16, 16, 16, 16, 16, 6, 17, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 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, 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/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 799) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CC1CCOCC1)c1cccc(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184485122 none O=C(N[C@@H](CC1CCOCC1)c1cccc(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 12, 12, 12, 12, 12, 5, 13, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485122 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 Building ZINC001184485122 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485122 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 798) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CC1CCOCC1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485122.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184485122 none O=C(N[C@@H](CC1CCOCC1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 13, 16, 16, 16, 16, 16, 6, 17, 17, 17, 17, 17, 17, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 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, 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/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 799) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CC1CCOCC1)c1cccc(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485122.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184485122 none O=C(N[C@@H](CC1CCOCC1)c1cccc(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 12, 12, 12, 12, 12, 5, 13, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 8, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485122 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485122 Building ZINC001184485132 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485132 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 800) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CC1CCOCC1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184485132 none O=C(N[C@H](CC1CCOCC1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 12, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 801) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CC1CCOCC1)c1cccc(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184485132 none O=C(N[C@H](CC1CCOCC1)c1cccc(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 14, 16, 16, 16, 16, 16, 6, 16, 16, 16, 16, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485132 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 Building ZINC001184485132 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485132 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 800) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CC1CCOCC1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485132.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184485132 none O=C(N[C@H](CC1CCOCC1)c1cccc(F)c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 12, 14, 14, 14, 14, 14, 6, 13, 13, 13, 13, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 13, 13, 13, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 801) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](CC1CCOCC1)c1cccc(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485132.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184485132 none O=C(N[C@H](CC1CCOCC1)c1cccc(F)c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 15, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 14, 16, 16, 16, 16, 16, 6, 16, 16, 16, 16, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485132 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485132 Building ZINC001184485178 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485178 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 802) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1OC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184485178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184485178 none COc1cc(C)ccc1OC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 28, 33, 33, 33, 16, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 803) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1OC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184485178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184485178 none COc1cc(C)ccc1OC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 39, 39, 39, 16, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 3, 3, 3, 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, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485178 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 Building ZINC001184485178 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485178 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 802) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1OC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184485178.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184485178 none COc1cc(C)ccc1OC1CCN(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 33, 28, 33, 33, 33, 16, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 34, 34, 34, 33, 33, 33, 33, 33, 33, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 803) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C)ccc1OC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1) `ZINC001184485178.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001184485178 none COc1cc(C)ccc1OC1CCN(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 39, 39, 39, 16, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 4, 4, 4, 3, 3, 3, 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, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485178 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485178 Building ZINC001184485206 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485206 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 804) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OC2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21) `ZINC001184485206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485206 none C[C@@H]1OC2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 805) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OC2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21) `ZINC001184485206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485206 none C[C@@H]1OC2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485206 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 Building ZINC001184485206 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485206 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 804) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OC2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21) `ZINC001184485206.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485206 none C[C@@H]1OC2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 5, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 805) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OC2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21) `ZINC001184485206.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485206 none C[C@@H]1OC2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 6, 6, 6, 6, 19, 19, 19, 19, 19, 19, 19, 19] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485206 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485206 Building ZINC001184485208 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485208 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 806) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21) `ZINC001184485208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485208 none C[C@H]1OC2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 16, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 807) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21) `ZINC001184485208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485208 none C[C@H]1OC2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485208 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 Building ZINC001184485208 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485208 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 806) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21) `ZINC001184485208.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485208 none C[C@H]1OC2(CCN(C(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 16, 6, 2, 7, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 16, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17] 50 rigid atoms, others: [10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 807) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1OC2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21) `ZINC001184485208.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001184485208 none C[C@H]1OC2(CCN(C(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)CC2)c2ccccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.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, 5, 7, 12, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 8, 1, 9, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 6, 6, 6, 20, 20, 20, 20, 20, 20, 20, 20] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485208 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485208 Building ZINC001184485223 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485223 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 808) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2ncc(Br)cc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184485223 none O=C(NCc1ccc2ncc(Br)cc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 37, 37, 37, 37, 37, 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 809) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2ncc(Br)cc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184485223 none O=C(NCc1ccc2ncc(Br)cc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 34, 34, 34, 34, 34, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485223 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 Building ZINC001184485223 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485223 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 808) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2ncc(Br)cc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485223.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184485223 none O=C(NCc1ccc2ncc(Br)cc2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 37, 37, 37, 37, 37, 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: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 809) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1ccc2ncc(Br)cc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485223.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001184485223 none O=C(NCc1ccc2ncc(Br)cc2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 8, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 15, 15, 34, 34, 34, 34, 34, 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: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485223 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485223 Building ZINC001184485242 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485242 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 810) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485242 none CC(C)(C)OC(=O)Nc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 21, 24, 19, 19, 19, 19, 19, 19, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 19, 19, 19, 19, 16, 16, 3, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 811) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485242 none CC(C)(C)OC(=O)Nc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 20, 22, 19, 19, 19, 18, 19, 19, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 19, 19, 19, 19, 16, 16, 3, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485242 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 Building ZINC001184485242 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485242 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 810) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485242.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485242 none CC(C)(C)OC(=O)Nc1ccccc1CNC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 21, 24, 19, 19, 19, 19, 19, 19, 16, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 21, 19, 19, 19, 19, 16, 16, 3, 4, 4, 4, 4] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 98 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 811) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)Nc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485242.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184485242 none CC(C)(C)OC(=O)Nc1ccccc1CNC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 20, 22, 19, 19, 19, 18, 19, 19, 16, 3, 3, 1, 3, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 31, 31, 31, 31, 31, 31, 31, 31, 31, 20, 19, 19, 19, 19, 16, 16, 3, 5, 5, 5, 5] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/281161/xco-8058088.67/working/building/ZINC001184485242 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485242 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485242 Building ZINC001184485255 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485255 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 812) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1) `ZINC001184485255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485255 none CN(C(=O)OC(C)(C)C)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 41, 41, 41, 42, 42, 42, 42, 9, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 9, 9, 2, 3, 3, 3, 3, 24, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 813) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1) `ZINC001184485255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485255 none CN(C(=O)OC(C)(C)C)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 41, 41, 41, 42, 42, 42, 42, 9, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 9, 9, 2, 3, 3, 3, 3, 24, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485255 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 Building ZINC001184485255 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485255 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 812) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1) `ZINC001184485255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485255 none CN(C(=O)OC(C)(C)C)c1ccc(CNC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 41, 41, 41, 42, 42, 42, 42, 9, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 9, 9, 2, 3, 3, 3, 3, 24, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 813) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1) `ZINC001184485255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485255 none CN(C(=O)OC(C)(C)C)c1ccc(CNC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)cc1 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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 41, 41, 41, 42, 42, 42, 42, 9, 24, 24, 9, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 24, 24, 41, 41, 41, 42, 42, 42, 42, 42, 42, 42, 42, 42, 24, 24, 9, 9, 2, 3, 3, 3, 3, 24, 24] 50 rigid atoms, others: [17, 18, 19, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485255 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485255 Building ZINC001184485266 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485266 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 814) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Cc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1) `ZINC001184485266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001184485266 none CCOC(=O)Cc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 31, 10, 31, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 32, 32, 32, 32, 32, 10, 10, 5, 5, 3, 4, 4, 4, 4, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 815) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Cc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1) `ZINC001184485266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001184485266 none CCOC(=O)Cc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 32, 32, 10, 32, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 33, 33, 33, 33, 33, 10, 10, 3, 5, 3, 4, 4, 4, 4, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485266 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 Building ZINC001184485266 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485266 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 814) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Cc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1) `ZINC001184485266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001184485266 none CCOC(=O)Cc1ccc(Cl)c(NC(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 31, 31, 10, 31, 5, 5, 5, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 32, 32, 32, 32, 32, 10, 10, 5, 5, 3, 4, 4, 4, 4, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 815) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)Cc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1) `ZINC001184485266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001184485266 none CCOC(=O)Cc1ccc(Cl)c(NC(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', '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, 1, 1, 1, 1, 16, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 32, 32, 10, 32, 5, 5, 3, 5, 5, 5, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 33, 33, 33, 33, 33, 10, 10, 3, 5, 3, 4, 4, 4, 4, 5] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485266 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485266 Building ZINC001184485305 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485305 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 816) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(N2CCC(F)(F)CC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485305 none O=C(Nc1ccc(N2CCC(F)(F)CC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 15, 15, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 3, 6, 34, 34, 33, 34, 34, 34, 34, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 817) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(N2CCC(F)(F)CC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485305 none O=C(Nc1ccc(N2CCC(F)(F)CC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 15, 15, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 3, 11, 33, 33, 33, 33, 33, 33, 33, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485305 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 Building ZINC001184485305 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485305 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 816) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(N2CCC(F)(F)CC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485305 none O=C(Nc1ccc(N2CCC(F)(F)CC2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 15, 15, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 3, 6, 34, 34, 33, 34, 34, 34, 34, 7, 7, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 7, 7, 34, 34, 34, 34, 34, 34, 34, 34, 7, 7, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 817) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(N2CCC(F)(F)CC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485305 none O=C(Nc1ccc(N2CCC(F)(F)CC2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 8, 5, 5, 5, 15, 15, 5, 5, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 6, 6, 3, 11, 33, 33, 33, 33, 33, 33, 33, 6, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 6, 6, 33, 33, 33, 33, 33, 33, 33, 33, 6, 6, 4, 4, 4, 4] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 69 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485305 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485305 Building ZINC001184485306 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485306 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 818) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(=O)C(F)(F)F)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485306 none COc1cccc(C(=O)C(F)(F)F)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 5, 15, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 15, 15, 15, 25, 25, 25, 25, 25, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 15, 15, 15, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 819) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(=O)C(F)(F)F)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485306 none COc1cccc(C(=O)C(F)(F)F)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 5, 15, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 6, 14, 14, 14, 24, 24, 24, 24, 24, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 14, 14, 14, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485306 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 Building ZINC001184485306 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485306 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 818) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(=O)C(F)(F)F)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485306 none COc1cccc(C(=O)C(F)(F)F)c1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 5, 15, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 15, 15, 15, 25, 25, 25, 25, 25, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 15, 15, 15, 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]) total number of confs: 94 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 819) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(=O)C(F)(F)F)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485306 none COc1cccc(C(=O)C(F)(F)F)c1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 11, 5, 15, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 14, 14, 6, 14, 14, 14, 24, 24, 24, 24, 24, 4, 4, 1, 4, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 16, 16, 16, 14, 14, 14, 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]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485306 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485306 Building ZINC001184485322 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485322 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 820) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2[nH]ccc2cc1Br)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184485322 none O=C(Nc1cc2[nH]ccc2cc1Br)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 26, 26, 26, 26, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 821) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2[nH]ccc2cc1Br)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184485322 none O=C(Nc1cc2[nH]ccc2cc1Br)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 24, 24, 24, 24, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485322 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 Building ZINC001184485322 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485322 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 820) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2[nH]ccc2cc1Br)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485322.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184485322 none O=C(Nc1cc2[nH]ccc2cc1Br)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 26, 26, 26, 26, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 48 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 821) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1cc2[nH]ccc2cc1Br)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485322.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001184485322 none O=C(Nc1cc2[nH]ccc2cc1Br)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 8, 6, 1, 1, 1, 1, 1, 17, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 24, 24, 24, 24, 9, 9, 9, 9] 50 rigid atoms, others: [16, 1, 14, 15] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485322 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485322 Building ZINC001184485538 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485538 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 822) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OCc1cc(Cl)ccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485538 none O=C(N1CCC2(CC1)OCc1cc(Cl)ccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 18, 18, 18, 18, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 823) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OCc1cc(Cl)ccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485538 none O=C(N1CCC2(CC1)OCc1cc(Cl)ccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485538 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 Building ZINC001184485538 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485538 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 822) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OCc1cc(Cl)ccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485538 none O=C(N1CCC2(CC1)OCc1cc(Cl)ccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 18, 18, 18, 18, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 823) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCC2(CC1)OCc1cc(Cl)ccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485538 none O=C(N1CCC2(CC1)OCc1cc(Cl)ccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 5, 5, 12, 5, 1, 1, 1, 16, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 18, 18, 18, 18, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 6] 50 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485538 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485538 Building ZINC001184485774 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485774 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 824) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2s1) `ZINC001184485774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485774 none COC(=O)c1cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 10, 16, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 16, 16, 16, 10, 10, 10, 10, 3, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 825) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cc2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2s1) `ZINC001184485774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485774 none COC(=O)c1cc2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 10, 16, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 16, 16, 16, 10, 10, 10, 10, 3, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485774 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 Building ZINC001184485774 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485774 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 824) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2s1) `ZINC001184485774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485774 none COC(=O)c1cc2cccc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 10, 16, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 16, 16, 16, 10, 10, 10, 10, 3, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 825) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cc2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2s1) `ZINC001184485774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001184485774 none COC(=O)c1cc2cccc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)c2s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'S.3', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 5, 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] 0 hydrogens 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, 10, 16, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 16, 16, 16, 10, 10, 10, 10, 3, 9, 9, 9, 9] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485774 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485774 Building ZINC001184485903 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485903 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 826) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccnc(O)c2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485903 none O=C(Nc1ccc(Oc2ccnc(O)c2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 12, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 8, 10, 11, 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: [3, 1, 3, 3, 5, 5, 5, 5, 25, 35, 35, 35, 35, 35, 35, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 35, 35, 70, 35, 5, 5, 4, 4, 4, 4] 100 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 827) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccnc(O)c2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485903 none O=C(Nc1ccc(Oc2ccnc(O)c2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 12, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 8, 10, 11, 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: [3, 1, 3, 3, 5, 5, 3, 3, 24, 35, 35, 35, 35, 35, 35, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 35, 35, 70, 35, 5, 5, 4, 4, 4, 4] 100 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485903 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 Building ZINC001184485903 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184485903 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 826) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccnc(O)c2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485903.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184485903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485903 none O=C(Nc1ccc(Oc2ccnc(O)c2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 12, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 8, 10, 11, 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: [3, 1, 3, 3, 5, 5, 5, 5, 25, 35, 35, 35, 35, 35, 35, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 35, 35, 70, 35, 5, 5, 4, 4, 4, 4] 100 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]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 827) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccnc(O)c2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184485903.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184485903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184485903 none O=C(Nc1ccc(Oc2ccnc(O)c2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 1, 1, 1, 8, 1, 12, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 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, 3, 7, 7, 7, 3, 7, 4, 7, 7, 7, 8, 10, 11, 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: [3, 1, 3, 3, 5, 5, 3, 3, 24, 35, 35, 35, 35, 35, 35, 5, 5, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 5, 5, 35, 35, 70, 35, 5, 5, 4, 4, 4, 4] 100 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]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184485903 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184485903 Building ZINC001184486125 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486125 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 828) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1[C@@H]2CCC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184486125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486125 none CC(C)(C)OC(=O)N1[C@@H]2CCC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 12, 12, 4, 8, 8, 8, 8, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 829) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1[C@@H]2CCC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184486125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486125 none CC(C)(C)OC(=O)N1[C@@H]2CCC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 3, 7, 7, 7, 7, 10, 10] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486125 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 Building ZINC001184486125 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486125 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 828) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1[C@@H]2CCC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184486125.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486125 none CC(C)(C)OC(=O)N1[C@@H]2CCC[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 12, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 12, 23, 23, 23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 12, 12, 12, 12, 12, 4, 8, 8, 8, 8, 12, 12] 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]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 829) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1[C@@H]2CCC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)C2) `ZINC001184486125.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486125 none CC(C)(C)OC(=O)N1[C@@H]2CCC[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])c1c[nH]c3ccc(Br)cc31)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', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 10, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 10, 3, 1, 3, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 10, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 10, 10, 10, 10, 10, 3, 7, 7, 7, 7, 10, 10] 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]) total number of confs: 76 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486125 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486125 Building ZINC001184486177 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486177 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 830) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[nH]c2cc(Br)ccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184486177 none O=C(NCc1c[nH]c2cc(Br)ccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 6, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 34, 34, 34, 34, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 831) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[nH]c2cc(Br)ccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184486177 none O=C(NCc1c[nH]c2cc(Br)ccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 6, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 34, 34, 34, 34, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486177 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 Building ZINC001184486177 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486177 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 830) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[nH]c2cc(Br)ccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486177.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184486177 none O=C(NCc1c[nH]c2cc(Br)ccc12)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 6, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 34, 34, 34, 34, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 831) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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[nH]c2cc(Br)ccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486177.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001184486177 none O=C(NCc1c[nH]c2cc(Br)ccc12)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 8, 6, 1, 1, 1, 17, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 34, 34, 34, 34, 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]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486177 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486177 Building ZINC001184486257 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184486257 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/832 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/833 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/833' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 834) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 835) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486257 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 Building ZINC001184486257 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184486257 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 832) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 833) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 834) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 835) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486257 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 Building ZINC001184486257 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184486257 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 832) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 833) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 834) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 835) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486257 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 Building ZINC001184486257 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184486257 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 832) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/832: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 833) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 834) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 835) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486257.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184486257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 62 natoms 61 natoms 60 natoms 59 names: ZINC001184486257 none O=C(N1CCCC2=C[C@H]3C[C@H](CN4CCCC[C@H]34)[C@@H]21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 1, 1, 5, 7, 5, 5, 7, 5, 10, 5, 5, 5, 5, 5, 7, 5, 7, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 36 rigid atoms, others: [24, 25, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486257 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486257 Building ZINC001184486280 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486280 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 836) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184486280 none COc1ccc(OC(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 837) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184486280 none COc1ccc(OC(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486280 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 Building ZINC001184486280 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486280 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 836) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486280.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184486280 none COc1ccc(OC(F)(F)F)cc1NC(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 837) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(OC(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486280.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001184486280 none COc1ccc(OC(F)(F)F)cc1NC(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 6, 6, 26, 26, 26, 26, 6, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 7, 7, 7, 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]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486280 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486280 Building ZINC001184486290 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486290 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 838) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(cccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184486290 none O=C(N1CCc2c(cccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 839) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(cccc2C(F)(F)F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184486290 none O=C(N1CCc2c(cccc2C(F)(F)F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486290 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 Building ZINC001184486290 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486290 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 838) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(cccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486290.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184486290 none O=C(N1CCc2c(cccc2C(F)(F)F)C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 839) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(cccc2C(F)(F)F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486290.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184486290 none O=C(N1CCc2c(cccc2C(F)(F)F)C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 9, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486290 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486290 Building ZINC001184486478 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486478 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 840) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3onc(c4ccccc4)c3C(=O)OC(C)(C)C)c2c1) `ZINC001184486478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486478 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3onc(c4ccccc4)c3C(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 17, 17, 26, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 6, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 841) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3onc(c4ccccc4)c3C(=O)OC(C)(C)C)c2c1) `ZINC001184486478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486478 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3onc(c4ccccc4)c3C(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 19, 19, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 3, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486478 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 Building ZINC001184486478 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486478 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 840) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3onc(c4ccccc4)c3C(=O)OC(C)(C)C)c2c1) `ZINC001184486478.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486478 none COc1ccc2[nH]cc([C@]([O-])([SiH3])C(=O)Nc3onc(c4ccccc4)c3C(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 8, 8, 4, 8, 8, 3, 3, 17, 17, 26, 27, 27, 27, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 6, 8, 8, 27, 27, 27, 27, 27, 27, 27, 27, 27, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 841) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3onc(c4ccccc4)c3C(=O)OC(C)(C)C)c2c1) `ZINC001184486478.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486478 none COc1ccc2[nH]cc([C@@]([O-])([SiH3])C(=O)Nc3onc(c4ccccc4)c3C(=O)OC(C)(C)C)c2c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.3', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 6, 1, 1, 5, 12, 1, 11, 8, 1, 12, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 12, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 8, 10, 11, 6, 4, 7, 3, 7, 7, 7, 7, 7, 7, 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, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 3, 3, 19, 19, 28, 28, 28, 28, 4, 4, 4, 4, 4, 4, 4, 4, 3, 9, 9, 3, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 4] 50 rigid atoms, others: [9, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486478 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486478 Building ZINC001184486688 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486688 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 842) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCOc2ccc(OC(F)(F)F)cc21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184486688 none O=C(N[C@@H]1CCOc2ccc(OC(F)(F)F)cc21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24, 26, 26, 26, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 843) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCOc2ccc(OC(F)(F)F)cc21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184486688 none O=C(N[C@@H]1CCOc2ccc(OC(F)(F)F)cc21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 28, 28, 28, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486688 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 Building ZINC001184486688 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486688 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 842) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCOc2ccc(OC(F)(F)F)cc21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184486688 none O=C(N[C@@H]1CCOc2ccc(OC(F)(F)F)cc21)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24, 26, 26, 26, 8, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 8, 8, 8, 8, 8, 8, 8, 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 843) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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]1CCOc2ccc(OC(F)(F)F)cc21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184486688 none O=C(N[C@@H]1CCOc2ccc(OC(F)(F)F)cc21)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 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', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 12, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 8, 8, 8, 8, 8, 8, 8, 8, 8, 26, 28, 28, 28, 8, 8, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486688 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486688 Building ZINC001184486718 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486718 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 844) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](OCc2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184486718 none O=C(N[C@H]1CC[C@@H](OCc2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 10, 10, 10, 10, 10, 18, 34, 36, 36, 36, 36, 36, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 10, 10, 34, 34, 36, 36, 36, 36, 36, 10, 10, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 845) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](OCc2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184486718 none O=C(N[C@H]1CC[C@@H](OCc2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 10, 10, 10, 10, 10, 17, 34, 35, 35, 34, 35, 35, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 10, 10, 34, 34, 35, 35, 34, 35, 35, 10, 10, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486718 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 Building ZINC001184486718 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486718 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 844) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](OCc2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486718.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184486718 none O=C(N[C@H]1CC[C@@H](OCc2ccccc2)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 10, 10, 10, 10, 10, 18, 34, 36, 36, 36, 36, 36, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 10, 10, 34, 34, 36, 36, 36, 36, 36, 10, 10, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 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/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 845) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](OCc2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184486718.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184486718 none O=C(N[C@H]1CC[C@@H](OCc2ccccc2)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 5, 5, 5, 7, 12, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 10, 10, 10, 10, 10, 10, 17, 34, 35, 35, 34, 35, 35, 10, 10, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 10, 10, 34, 34, 35, 35, 34, 35, 35, 10, 10, 10, 10, 4, 4, 4, 4] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486718 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486718 Building ZINC001184486804 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184486804 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/846 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 19, 19, 16, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/281161/xco-8058088.67/working/3D/847 `/scratch/xiaobo/281161/xco-8058088.67/working/3D/847' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 8, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 17, 17, 17, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 848) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 19, 19, 16, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 849) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 8, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 17, 17, 17, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486804 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 Building ZINC001184486804 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184486804 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 846) grep: /scratch/xiaobo/281161/xco-8058088.67/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: N[C@H]1CC[C@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 8, 14, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 19, 19, 19, 19, 19, 23, 23, 19, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 19, 19, 23, 23, 23, 23, 23, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 847) grep: /scratch/xiaobo/281161/xco-8058088.67/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: N[C@H]1CC[C@@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 848) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 19, 19, 16, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 849) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 8, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 17, 17, 17, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486804 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 Building ZINC001184486804 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184486804 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 846) grep: /scratch/xiaobo/281161/xco-8058088.67/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: N[C@H]1CC[C@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 8, 14, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 19, 19, 19, 19, 19, 23, 23, 19, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 19, 19, 23, 23, 23, 23, 23, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 847) grep: /scratch/xiaobo/281161/xco-8058088.67/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: N[C@H]1CC[C@@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 848) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 19, 19, 16, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 849) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 8, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 17, 17, 17, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486804 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 Building ZINC001184486804 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001184486804 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 846) grep: /scratch/xiaobo/281161/xco-8058088.67/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: N[C@H]1CC[C@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 8, 14, 5, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 19, 19, 19, 19, 19, 23, 23, 19, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 5, 5, 5, 5, 19, 19, 23, 23, 23, 23, 23, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 847) grep: /scratch/xiaobo/281161/xco-8058088.67/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: N[C@H]1CC[C@@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@@H](N(C(=O)[C@@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 6, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 19, 19, 19, 19, 19, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 78 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `2' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 2 (index: 848) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 6, 10, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 7, 15, 15, 15, 15, 15, 19, 19, 16, 19, 19, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 15, 15, 19, 19, 19, 19, 19, 10, 10, 10, 10] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `3' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 3 (index: 849) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N[C@H]1CC[C@@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1) `ZINC001184486804.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001184486804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 10 0 4 10 1 4 10 2 3 10 2 13 to be deleted 14 to be deleted 15 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001184486804 none N[C@H]1CC[C@@H](N(C(=O)[C@]([O-])([SiH3])c2c[nH]c3ccc(Br)cc32)[C@@H]2C[C@H]2c2ccccc2)CC1 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'H', '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', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [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, 7, 7, 7] 0 hydrogens 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, 8, 11, 3, 1, 3, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 8, 17, 17, 17, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6, 17, 17, 22, 22, 17, 22, 22, 11, 11, 11, 11] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/281161/xco-8058088.67/working/building/ZINC001184486804 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486804 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/1.* 3: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/3.* 2: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/2.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486804 Building ZINC001184486947 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486947 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 850) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc2o1) `ZINC001184486947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001184486947 none CCOC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 12, 24, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 35, 35, 35, 35, 35, 12, 12, 3, 4, 4, 4, 4, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 851) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc2o1) `ZINC001184486947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001184486947 none CCOC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 12, 24, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 35, 35, 35, 35, 35, 12, 12, 3, 4, 4, 4, 4, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486947 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 Building ZINC001184486947 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184486947 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 850) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc2o1) `ZINC001184486947.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184486947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001184486947 none CCOC(=O)c1cc2cc(NC(=O)[C@@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 12, 24, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 35, 35, 35, 35, 35, 12, 12, 3, 4, 4, 4, 4, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 851) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc2o1) `ZINC001184486947.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184486947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001184486947 none CCOC(=O)c1cc2cc(NC(=O)[C@]([O-])([SiH3])c3c[nH]c4ccc(Br)cc43)ccc2o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [35, 24, 24, 12, 24, 12, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 12, 35, 35, 35, 35, 35, 12, 12, 3, 4, 4, 4, 4, 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]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184486947 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184486947 Building ZINC001184487017 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487017 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 852) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(OCc2ccncc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487017 none O=C(Nc1ccc(OCc2ccncc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 7, 14, 14, 27, 27, 27, 27, 27, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 14, 14, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 853) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(OCc2ccncc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487017 none O=C(Nc1ccc(OCc2ccncc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 6, 7, 14, 14, 28, 28, 14, 28, 28, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 14, 14, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487017 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 Building ZINC001184487017 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487017 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 852) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(OCc2ccncc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487017.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487017 none O=C(Nc1ccc(OCc2ccncc2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 7, 7, 14, 14, 27, 27, 27, 27, 27, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 14, 14, 27, 27, 27, 27, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 853) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(OCc2ccncc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487017.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487017 none O=C(Nc1ccc(OCc2ccncc2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 12, 5, 1, 1, 1, 8, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 7, 7, 6, 7, 14, 14, 28, 28, 14, 28, 28, 7, 7, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 14, 14, 28, 28, 28, 28, 7, 7, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487017 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487017 Building ZINC001184487026 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487026 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 854) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nc(c3ccccc3)sc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487026 none O=C(N1Cc2nc(c3ccccc3)sc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 15, 15, 15, 15, 15, 17, 17, 17, 17, 17, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 17, 17, 17, 17, 17, 15, 15, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 855) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nc(c3ccccc3)sc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487026 none O=C(N1Cc2nc(c3ccccc3)sc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 15, 15, 15, 15, 15, 17, 17, 17, 17, 17, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 17, 17, 17, 17, 17, 15, 15, 9, 9, 9, 9] 49 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: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487026 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 Building ZINC001184487026 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487026 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 854) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nc(c3ccccc3)sc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487026.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487026 none O=C(N1Cc2nc(c3ccccc3)sc2C1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 15, 15, 15, 15, 15, 17, 17, 17, 17, 17, 15, 15, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 17, 17, 17, 17, 17, 15, 15, 7, 7, 7, 7] 50 rigid atoms, others: [16, 1, 18, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 855) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1Cc2nc(c3ccccc3)sc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487026.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487026 none O=C(N1Cc2nc(c3ccccc3)sc2C1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 1, 14, 1, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 15, 15, 15, 15, 15, 17, 17, 17, 17, 17, 15, 15, 15, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 15, 15, 17, 17, 17, 17, 17, 15, 15, 9, 9, 9, 9] 49 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: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487026 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487026 Building ZINC001184487622 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487622 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 856) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cnn([C@@H]3CCCCO3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487622 none O=C(Nc1ccc2cnn([C@@H]3CCCCO3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 13, 13, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 857) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cnn([C@@H]3CCCCO3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487622 none O=C(Nc1ccc2cnn([C@@H]3CCCCO3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 13, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487622 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 Building ZINC001184487622 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487622 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 856) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cnn([C@@H]3CCCCO3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487622.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487622 none O=C(Nc1ccc2cnn([C@@H]3CCCCO3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 13, 13, 13, 13, 13, 13, 13, 29, 29, 29, 29, 29, 29, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 13, 29, 29, 29, 29, 29, 29, 29, 29, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 857) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cnn([C@@H]3CCCCO3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487622.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487622 none O=C(Nc1ccc2cnn([C@@H]3CCCCO3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 13, 13, 13, 13, 13, 13, 13, 28, 28, 28, 28, 28, 28, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487622 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487622 Building ZINC001184487624 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487624 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 858) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cnn([C@H]3CCCCO3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487624 none O=C(Nc1ccc2cnn([C@H]3CCCCO3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 13, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 13, 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 859) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cnn([C@H]3CCCCO3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487624 none O=C(Nc1ccc2cnn([C@H]3CCCCO3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 13, 13, 13, 13, 13, 13, 13, 30, 30, 30, 30, 30, 30, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487624 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 Building ZINC001184487624 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487624 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 858) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cnn([C@H]3CCCCO3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487624.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487624 none O=C(Nc1ccc2cnn([C@H]3CCCCO3)c2c1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 13, 13, 13, 13, 13, 13, 13, 26, 26, 26, 26, 26, 26, 13, 13, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 13, 26, 26, 26, 26, 26, 26, 26, 26, 13, 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: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 859) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(Nc1ccc2cnn([C@H]3CCCCO3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487624.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 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: ZINC001184487624 none O=C(Nc1ccc2cnn([C@H]3CCCCO3)c2c1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 1, 1, 1, 1, 1, 8, 8, 5, 7, 5, 5, 5, 5, 12, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 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] 0 hydrogens need rotated 50 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, 13, 13, 13, 13, 13, 13, 13, 30, 30, 30, 30, 30, 30, 13, 13, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 13, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 13, 5, 5, 5, 5] 50 rigid atoms, others: [1, 19, 20, 21] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487624 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487624 Building ZINC001184487342 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487342 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 860) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccccn2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487342 none O=C(NCc1ccc(Oc2ccccn2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 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, 16, 16, 10, 13, 35, 37, 37, 37, 37, 37, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 37, 37, 37, 37, 16, 16, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 861) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccccn2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487342 none O=C(NCc1ccc(Oc2ccccn2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 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, 16, 16, 10, 10, 32, 36, 36, 36, 36, 36, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 36, 36, 36, 36, 16, 16, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487342 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 Building ZINC001184487342 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487342 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 860) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccccn2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487342 none O=C(NCc1ccc(Oc2ccccn2)cc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 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, 16, 16, 10, 13, 35, 37, 37, 37, 37, 37, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 37, 37, 37, 37, 16, 16, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 861) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(Oc2ccccn2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487342 none O=C(NCc1ccc(Oc2ccccn2)cc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 8, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 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] 0 hydrogens need rotated 50 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, 16, 16, 10, 10, 32, 36, 36, 36, 36, 36, 16, 16, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 10, 10, 16, 16, 36, 36, 36, 36, 16, 16, 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]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487342 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487342 Building ZINC001184487410 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487410 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 862) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc2ccccc2n1Cc1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184487410 none O=C(NCc1nc2ccccc2n1Cc1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 863) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc2ccccc2n1Cc1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184487410 none O=C(NCc1nc2ccccc2n1Cc1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487410 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 Building ZINC001184487410 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487410 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 862) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc2ccccc2n1Cc1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184487410 none O=C(NCc1nc2ccccc2n1Cc1ccccc1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 13, 18, 18, 18, 18, 18, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 18, 18, 18, 18, 25, 25, 25, 25, 25, 25, 25, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 101 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 863) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCc1nc2ccccc2n1Cc1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 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: ZINC001184487410 none O=C(NCc1nc2ccccc2n1Cc1ccccc1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 1, 1, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 13, 13, 17, 17, 17, 17, 24, 24, 24, 24, 24, 24, 24, 6, 6, 6, 6] 50 rigid atoms, others: [1, 20, 21, 22] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487410 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487410 Building ZINC001184487422 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487422 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 864) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1ccncc1C(F)(F)F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184487422 none O=C(N[C@H](c1ccncc1C(F)(F)F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 17, 17, 11, 17, 17, 17, 17, 17, 17, 11, 18, 18, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 17, 17, 17, 18, 18, 18, 18, 18, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 865) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1ccncc1C(F)(F)F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184487422 none O=C(N[C@H](c1ccncc1C(F)(F)F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 18, 18, 11, 18, 18, 18, 18, 18, 18, 11, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 18, 18, 18, 17, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 98 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487422 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 Building ZINC001184487422 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487422 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 864) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1ccncc1C(F)(F)F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184487422 none O=C(N[C@H](c1ccncc1C(F)(F)F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 17, 17, 11, 17, 17, 17, 17, 17, 17, 11, 18, 18, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 17, 17, 17, 18, 18, 18, 18, 18, 8, 8, 8, 8] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 100 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 865) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1ccncc1C(F)(F)F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184487422 none O=C(N[C@H](c1ccncc1C(F)(F)F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 18, 18, 11, 18, 18, 18, 18, 18, 18, 11, 17, 17, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 18, 18, 18, 17, 17, 17, 17, 17, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 98 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487422 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487422 Building ZINC001184487423 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487423 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 866) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1ccncc1C(F)(F)F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184487423 none O=C(N[C@@H](c1ccncc1C(F)(F)F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 15, 15, 12, 15, 15, 15, 15, 15, 15, 11, 13, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 15, 15, 15, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 867) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1ccncc1C(F)(F)F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184487423 none O=C(N[C@@H](c1ccncc1C(F)(F)F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 18, 18, 14, 18, 18, 18, 18, 18, 18, 13, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 18, 18, 18, 17, 17, 17, 17, 17, 9, 9, 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, 43]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487423 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 Building ZINC001184487423 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487423 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 866) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1ccncc1C(F)(F)F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184487423 none O=C(N[C@@H](c1ccncc1C(F)(F)F)C1CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 11, 11, 15, 15, 12, 15, 15, 15, 15, 15, 15, 11, 13, 13, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 15, 15, 15, 13, 13, 13, 13, 13, 7, 7, 7, 7] 50 rigid atoms, others: [1, 18, 19, 20] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 67 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 867) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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](c1ccncc1C(F)(F)F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 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: ZINC001184487423 none O=C(N[C@@H](c1ccncc1C(F)(F)F)C1CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 7, 1, 1, 1, 8, 1, 1, 5, 15, 15, 15, 5, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 13, 13, 18, 18, 14, 18, 18, 18, 18, 18, 18, 13, 17, 17, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 18, 18, 18, 17, 17, 17, 17, 17, 9, 9, 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, 43]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487423 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487423 Building ZINC001184487743 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487743 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 868) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccc(OC(F)(F)F)c1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487743 none CN(Cc1cccc(OC(F)(F)F)c1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 38, 38, 38, 38, 9, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 869) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccc(OC(F)(F)F)c1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487743 none CN(Cc1cccc(OC(F)(F)F)c1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 39, 39, 39, 39, 10, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 10, 10, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487743 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 Building ZINC001184487743 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487743 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 868) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccc(OC(F)(F)F)c1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487743 none CN(Cc1cccc(OC(F)(F)F)c1)C(=O)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 9, 9, 9, 9, 38, 38, 38, 38, 9, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 869) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cccc(OC(F)(F)F)c1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001184487743 none CN(Cc1cccc(OC(F)(F)F)c1)C(=O)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 12, 5, 15, 15, 15, 1, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 10, 10, 10, 10, 39, 39, 39, 39, 10, 1, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 10, 10, 10, 10, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487743 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487743 Building ZINC001184487802 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487802 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 870) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(n2ccc3ccccc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487802 none O=C(N1CCC(n2ccc3ccccc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 871) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(n2ccc3ccccc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487802 none O=C(N1CCC(n2ccc3ccccc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487802 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 Building ZINC001184487802 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001184487802 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 870) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(n2ccc3ccccc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487802.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001184487802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487802 none O=C(N1CCC(n2ccc3ccccc32)CC1)[C@@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 11, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 15, 15, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 15, 15, 15, 15, 5, 5, 5, 5] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 871) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,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(n2ccc3ccccc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21) `ZINC001184487802.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001184487802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001184487802 none O=C(N1CCC(n2ccc3ccccc32)CC1)[C@]([O-])([SiH3])c1c[nH]c2ccc(Br)cc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 1, 17, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 10, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 25, 25, 12, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 12, 12, 12, 12, 12, 25, 25, 25, 25, 25, 25, 12, 12, 12, 12, 6, 6, 6, 6] 50 rigid atoms, others: [1, 18, 19, 17] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001184487802 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001184487802 Building ZINC000105471001 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105471001 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 872) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCc1ccc(C)cc1) `ZINC000105471001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105471001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105471001 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCc1ccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 6, 6, 6, 6, 6, 6, 10, 8, 8, 25, 35, 35, 32, 35, 35, 35, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 4, 6, 6, 6, 6, 10, 26, 26, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 164 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 873) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCc1ccc(C)cc1) `ZINC000105471001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105471001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105471001 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCc1ccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 6, 6, 6, 6, 6, 6, 10, 8, 8, 24, 35, 35, 28, 35, 35, 35, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 4, 6, 6, 6, 6, 10, 25, 25, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 185 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000105471001 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 Building ZINC000105471001 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105471001 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 872) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCc1ccc(C)cc1) `ZINC000105471001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105471001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105471001 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCc1ccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 6, 6, 6, 6, 6, 6, 10, 8, 8, 25, 35, 35, 32, 35, 35, 35, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 4, 6, 6, 6, 6, 10, 26, 26, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 164 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 873) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCc1ccc(C)cc1) `ZINC000105471001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105471001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000105471001 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)NCc1ccc(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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 4, 6, 6, 6, 6, 6, 6, 10, 8, 8, 24, 35, 35, 28, 35, 35, 35, 3, 3, 3, 8, 8, 6, 8, 8, 3, 3, 3, 4, 6, 6, 6, 6, 10, 25, 25, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 185 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000105471001 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105471001 Building ZINC000105495113 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105495113 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 874) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1cccc(C)c1) `ZINC000105495113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105495113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000105495113 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 11, 9, 9, 32, 32, 28, 32, 32, 32, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 5, 9, 9, 9, 9, 11, 32, 32, 31, 32, 32, 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]) total number of confs: 102 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 875) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1cccc(C)c1) `ZINC000105495113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105495113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000105495113 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 10, 10, 10, 10, 10, 10, 12, 10, 10, 33, 33, 10, 33, 33, 33, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 3, 5, 10, 10, 10, 10, 12, 33, 33, 10, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000105495113 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 Building ZINC000105495113 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000105495113 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 874) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1cccc(C)c1) `ZINC000105495113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000105495113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000105495113 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 11, 9, 9, 32, 32, 28, 32, 32, 32, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 5, 9, 9, 9, 9, 11, 32, 32, 31, 32, 32, 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]) total number of confs: 102 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 875) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1cccc(C)c1) `ZINC000105495113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000105495113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000105495113 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1C(=O)Nc1cccc(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 5, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 5, 10, 10, 10, 10, 10, 10, 12, 10, 10, 33, 33, 10, 33, 33, 33, 3, 3, 3, 9, 9, 5, 9, 9, 3, 3, 3, 5, 10, 10, 10, 10, 12, 33, 33, 10, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 133 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000105495113 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000105495113 Building ZINC000409566355 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409566355 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 876) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@H]1c1ccccc1) `ZINC000409566355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409566355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566355 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 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, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 877) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@H]1c1ccccc1) `ZINC000409566355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409566355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566355 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409566355 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 Building ZINC000409566355 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409566355 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 876) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@H]1c1ccccc1) `ZINC000409566355.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409566355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566355 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 10, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 10, 10, 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, 58, 59, 60]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 877) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@H]1c1ccccc1) `ZINC000409566355.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409566355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566355 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409566355 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566355 Building ZINC000409566356 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409566356 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 878) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@H]1c1ccccc1) `ZINC000409566356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409566356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566356 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 10, 12, 3, 3, 3, 2, 10, 10, 11, 11, 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, 58, 59, 60]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 879) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@H]1c1ccccc1) `ZINC000409566356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409566356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566356 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 11, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409566356 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 Building ZINC000409566356 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409566356 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 878) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@H]1c1ccccc1) `ZINC000409566356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409566356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566356 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 12, 12, 10, 12, 3, 3, 3, 2, 10, 10, 11, 11, 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, 58, 59, 60]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 879) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@H]1c1ccccc1) `ZINC000409566356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409566356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566356 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCO[C@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 11, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 54 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409566356 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566356 Building ZINC000409566357 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409566357 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 880) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@@H]1c1ccccc1) `ZINC000409566357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409566357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 11, 11, 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, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 881) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@@H]1c1ccccc1) `ZINC000409566357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409566357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409566357 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 Building ZINC000409566357 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409566357 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 880) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@@H]1c1ccccc1) `ZINC000409566357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409566357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 11, 11, 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, 58, 59, 60]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 881) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@@H]1c1ccccc1) `ZINC000409566357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409566357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 6, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 12, 12, 12, 12, 3, 3, 3, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/281161/xco-8058088.67/working/building/ZINC000409566357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409566357 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566357 Building ZINC000409566358 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409566358 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 882) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@@H]1c1ccccc1) `ZINC000409566358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409566358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566358 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 883) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@@H]1c1ccccc1) `ZINC000409566358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409566358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566358 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409566358 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 Building ZINC000409566358 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409566358 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 882) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@@H]1c1ccccc1) `ZINC000409566358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409566358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566358 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 2, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 883) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO[C@@H]1c1ccccc1) `ZINC000409566358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409566358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000409566358 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCO[C@@H]1c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.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', 'H', 'H'] dock atom type 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, 12, 5, 7, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 10, 10, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409566358 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409566358 Building ZINC000409737529 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409737529 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 884) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCCc1nc(c2ccncc2)cs1) `ZINC000409737529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409737529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000409737529 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(c2ccncc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 8, 1, 1, 1, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 13, 13, 13, 17, 17, 13, 17, 17, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 4, 4, 6, 6, 17, 17, 17, 17, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 885) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCCc1nc(c2ccncc2)cs1) `ZINC000409737529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409737529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000409737529 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(c2ccncc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 8, 1, 1, 1, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 13, 13, 16, 16, 13, 16, 16, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 5, 7, 7, 16, 16, 16, 16, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409737529 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 Building ZINC000409737529 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409737529 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 884) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCCc1nc(c2ccncc2)cs1) `ZINC000409737529.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409737529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000409737529 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)NCCc1nc(c2ccncc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 8, 1, 1, 1, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 6, 13, 13, 13, 17, 17, 13, 17, 17, 13, 13, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 2, 4, 4, 6, 6, 17, 17, 17, 17, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 885) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)NCCc1nc(c2ccncc2)cs1) `ZINC000409737529.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409737529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000409737529 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)NCCc1nc(c2ccncc2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 8, 1, 1, 1, 1, 8, 1, 1, 1, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 7, 13, 13, 13, 16, 16, 13, 16, 16, 13, 13, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 5, 7, 7, 16, 16, 16, 16, 13] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409737529 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409737529 Building ZINC000409895742 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409895742 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 886) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3I)c(C)c2)cc1) `ZINC000409895742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409895742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000409895742 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3I)c(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 2, 8, 32, 30, 32, 50, 50, 50, 50, 50, 50, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 31, 50, 50, 50, 50, 10, 10, 10, 10, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 887) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3I)c(C)c2)cc1) `ZINC000409895742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409895742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000409895742 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3I)c(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 2, 2, 24, 26, 27, 50, 50, 30, 50, 50, 50, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 23, 50, 50, 47, 50, 10, 10, 10, 10, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409895742 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 Building ZINC000409895742 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409895742 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 886) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3I)c(C)c2)cc1) `ZINC000409895742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409895742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000409895742 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3I)c(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 2, 8, 32, 30, 32, 50, 50, 50, 50, 50, 50, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 31, 50, 50, 50, 50, 10, 10, 10, 10, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 887) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3I)c(C)c2)cc1) `ZINC000409895742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409895742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC000409895742 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(NC(=O)c3ccccc3I)c(C)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'I', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 18, 1, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 10, 10, 2, 2, 24, 26, 27, 50, 50, 30, 50, 50, 50, 10, 10, 10, 3, 3, 3, 3, 3, 3, 3, 2, 10, 10, 23, 50, 50, 47, 50, 10, 10, 10, 10, 3, 3] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409895742 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409895742 Building ZINC000409976743 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409976743 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 888) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)Cc1cccs1) `ZINC000409976743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409976743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000409976743 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 3, 6, 6, 6, 8, 8, 8, 32, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 6, 6, 6, 6, 8, 32, 32, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 889) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)Cc1cccs1) `ZINC000409976743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409976743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000409976743 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 3, 6, 6, 6, 8, 8, 8, 32, 49, 49, 49, 49, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 6, 6, 8, 32, 32, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409976743 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 Building ZINC000409976743 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000409976743 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 888) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)Cc1cccs1) `ZINC000409976743.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000409976743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000409976743 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 3, 6, 6, 6, 8, 8, 8, 32, 49, 49, 49, 49, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 2, 6, 6, 6, 6, 8, 32, 32, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 889) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)Cc1cccs1) `ZINC000409976743.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000409976743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC000409976743 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1NC(=O)Cc1cccs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 3, 6, 6, 6, 8, 8, 8, 32, 49, 49, 49, 49, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 2, 6, 6, 6, 6, 8, 32, 32, 49, 49, 49] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000409976743 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000409976743 Building ZINC000410054244 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410054244 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 890) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2c[nH]c3ncccc23)CC1) `ZINC000410054244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410054244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410054244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ncccc23)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', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type 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, 8, 6, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 3, 3, 3, 3, 3, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 43 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 891) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2c[nH]c3ncccc23)CC1) `ZINC000410054244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410054244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410054244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ncccc23)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', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type 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, 8, 6, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 4, 4, 4, 4, 4, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 44 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000410054244 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 Building ZINC000410054244 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410054244 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 890) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2c[nH]c3ncccc23)CC1) `ZINC000410054244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410054244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410054244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ncccc23)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', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type 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, 8, 6, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 2, 2, 2, 12, 12, 2, 12, 2, 2, 2, 3, 3, 3, 3, 3, 9, 9, 9, 9, 3, 3, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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: 43 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 891) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2c[nH]c3ncccc23)CC1) `ZINC000410054244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410054244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000410054244 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2c[nH]c3ncccc23)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', 'N.pl3', 'H', 'C.ar', 'N.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'] dock atom type 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, 8, 6, 1, 8, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 4, 4, 4, 4, 4, 12, 12, 12, 12, 4, 4, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 44 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000410054244 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410054244 Building ZINC000410091233 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410091233 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 892) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C)nn(c3cccc(C(F)(F)F)c3)c2C)n(Cc2ccccc2)n1) `ZINC000410091233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410091233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000410091233 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n(Cc2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'N.pl3', 'C.3', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 9, 10, 10, 9, 10, 10, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 9, 9, 10, 10, 10, 10, 10] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 893) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C)nn(c3cccc(C(F)(F)F)c3)c2C)n(Cc2ccccc2)n1) `ZINC000410091233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410091233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000410091233 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n(Cc2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'N.pl3', 'C.3', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 9, 9, 10, 10, 10, 10, 10] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000410091233 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 Building ZINC000410091233 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410091233 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 892) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C)nn(c3cccc(C(F)(F)F)c3)c2C)n(Cc2ccccc2)n1) `ZINC000410091233.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410091233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000410091233 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n(Cc2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'N.pl3', 'C.3', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 9, 10, 10, 9, 10, 10, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 9, 9, 10, 10, 10, 10, 10] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 893) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C)nn(c3cccc(C(F)(F)F)c3)c2C)n(Cc2ccccc2)n1) `ZINC000410091233.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410091233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000410091233 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3cccc(C(F)(F)F)c3)c2C)n(Cc2ccccc2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.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', 'N.pl3', 'C.3', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 5, 1, 1, 1, 1, 1, 1, 8, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 4, 4, 9, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 9, 9, 10, 10, 10, 10, 10] 50 rigid atoms, others: [4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000410091233 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410091233 Building ZINC000410282289 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410282289 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 894) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccccc2F)C1) `ZINC000410282289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410282289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000410282289 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 12, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 8, 4, 3, 3, 3, 13, 13, 12, 13, 3, 3, 3, 4, 4, 4, 4, 8, 8, 7, 8, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 45 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 895) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccccc2F)C1) `ZINC000410282289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410282289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000410282289 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 10, 10, 5, 10, 10, 10, 3, 2, 2, 2, 16, 16, 7, 16, 2, 2, 2, 3, 3, 3, 3, 10, 10, 10, 10, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000410282289 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 Building ZINC000410282289 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410282289 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 894) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccccc2F)C1) `ZINC000410282289.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410282289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000410282289 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 12, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 8, 4, 3, 3, 3, 13, 13, 12, 13, 3, 3, 3, 4, 4, 4, 4, 8, 8, 7, 8, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 45 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 895) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccccc2F)C1) `ZINC000410282289.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410282289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000410282289 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](c2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 10, 10, 5, 10, 10, 10, 3, 2, 2, 2, 16, 16, 7, 16, 2, 2, 2, 3, 3, 3, 3, 10, 10, 10, 10, 3, 3] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000410282289 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282289 Building ZINC000410282291 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410282291 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 896) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccccc2F)C1) `ZINC000410282291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410282291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000410282291 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 9, 4, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 4, 4, 4, 4, 9, 9, 8, 9, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 62 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 897) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccccc2F)C1) `ZINC000410282291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410282291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000410282291 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 5, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 9, 4, 3, 3, 3, 12, 12, 5, 12, 3, 3, 3, 4, 4, 4, 4, 9, 9, 8, 9, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000410282291 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 Building ZINC000410282291 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000410282291 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 896) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccccc2F)C1) `ZINC000410282291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000410282291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000410282291 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 12, 12, 2, 12, 12, 12, 12, 12, 12, 2, 2, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 9, 4, 2, 2, 2, 12, 12, 8, 12, 2, 2, 2, 4, 4, 4, 4, 9, 9, 8, 9, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 62 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 897) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccccc2F)C1) `ZINC000410282291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000410282291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000410282291 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](c2ccccc2F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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, 7, 1, 1, 1, 1, 1, 1, 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, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 5, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 9, 4, 3, 3, 3, 12, 12, 5, 12, 3, 3, 3, 4, 4, 4, 4, 9, 9, 8, 9, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 58 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000410282291 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000410282291 Building ZINC000634307861 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000634307861 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 898) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccccc3Cl)c2)cc1) `ZINC000634307861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000634307861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000634307861 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccccc3Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', '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, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 15, 4, 10, 15, 15, 24, 24, 24, 35, 50, 50, 37, 50, 50, 50, 15, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 50, 50, 50, 50, 15, 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: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 899) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccccc3Cl)c2)cc1) `ZINC000634307861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000634307861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000634307861 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccccc3Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', '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, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 15, 10, 15, 15, 15, 24, 24, 24, 35, 50, 50, 48, 50, 50, 50, 15, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 50, 50, 50, 50, 15, 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000634307861 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 Building ZINC000634307861 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000634307861 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 898) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccccc3Cl)c2)cc1) `ZINC000634307861.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000634307861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000634307861 none Cc1ccc([C@@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccccc3Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', '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, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 15, 4, 10, 15, 15, 24, 24, 24, 35, 50, 50, 37, 50, 50, 50, 15, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 50, 50, 50, 50, 15, 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: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 899) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccccc3Cl)c2)cc1) `ZINC000634307861.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000634307861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC000634307861 none Cc1ccc([C@]([O-])([SiH3])C(=O)Nc2ccc(Cl)c(S(=O)(=O)Nc3ccccc3Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', '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', '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, 1, 16, 1, 14, 11, 11, 8, 1, 1, 1, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 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: [1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 15, 15, 10, 15, 15, 15, 24, 24, 24, 35, 50, 50, 48, 50, 50, 50, 15, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 35, 50, 50, 50, 50, 15, 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: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000634307861 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000634307861 Building ZINC000636445056 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000636445056 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 900) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(C(=O)N2CCCC2)cc1) `ZINC000636445056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000636445056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000636445056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC2)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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 2, 12, 12, 12, 12, 12, 12, 5, 5, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 901) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(C(=O)N2CCCC2)cc1) `ZINC000636445056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000636445056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000636445056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC2)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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 4, 11, 11, 12, 12, 12, 11, 5, 5, 3, 3, 3, 15, 15, 5, 15, 3, 3, 3, 2, 5, 5, 12, 12, 12, 12, 12, 12, 11, 11, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000636445056 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 Building ZINC000636445056 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000636445056 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 900) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(C(=O)N2CCCC2)cc1) `ZINC000636445056.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000636445056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000636445056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC2)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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 2, 12, 12, 12, 12, 12, 12, 5, 5, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 2, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 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: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 901) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(C(=O)N2CCCC2)cc1) `ZINC000636445056.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000636445056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000636445056 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)N2CCCC2)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', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 5, 5, 2, 4, 11, 11, 12, 12, 12, 11, 5, 5, 3, 3, 3, 15, 15, 5, 15, 3, 3, 3, 2, 5, 5, 12, 12, 12, 12, 12, 12, 11, 11, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 83 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000636445056 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000636445056 Building ZINC000637358998 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000637358998 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 902) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)NC2CC2)cc1) `ZINC000637358998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000637358998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000637358998 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)NC2CC2)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 14, 15, 14, 14, 16, 16, 5, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 5, 14, 14, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 903) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)NC2CC2)cc1) `ZINC000637358998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000637358998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000637358998 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)NC2CC2)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 2, 2, 13, 14, 13, 13, 15, 15, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 4, 4, 13, 13, 15, 15, 15, 15, 15, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000637358998 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 Building ZINC000637358998 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000637358998 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 902) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)NC2CC2)cc1) `ZINC000637358998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000637358998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000637358998 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)NC2CC2)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 2, 2, 14, 15, 14, 14, 16, 16, 5, 5, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 2, 5, 5, 14, 14, 16, 16, 16, 16, 16, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 903) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(NC(=O)NC2CC2)cc1) `ZINC000637358998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000637358998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000637358998 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(NC(=O)NC2CC2)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', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 11, 8, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 2, 2, 13, 14, 13, 13, 15, 15, 4, 4, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 2, 4, 4, 13, 13, 15, 15, 15, 15, 15, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000637358998 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000637358998 Building ZINC000641237427 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641237427 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 904) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(C(=O)NC(C)(C)C)cc1) `ZINC000641237427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641237427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000641237427 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 4, 4, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 905) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(C(=O)NC(C)(C)C)cc1) `ZINC000641237427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641237427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000641237427 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 12, 12, 12, 12, 12, 12, 4, 4, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 2, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000641237427 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 Building ZINC000641237427 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000641237427 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 904) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(C(=O)NC(C)(C)C)cc1) `ZINC000641237427.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000641237427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000641237427 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 4, 4, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 2, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 61 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 905) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(C(=O)NC(C)(C)C)cc1) `ZINC000641237427.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000641237427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000641237427 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(C(=O)NC(C)(C)C)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 2, 2, 12, 12, 12, 12, 12, 12, 4, 4, 3, 3, 3, 13, 13, 6, 13, 3, 3, 3, 2, 4, 4, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 4, 4] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 77 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000641237427 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000641237427 Building ZINC000642042452 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642042452 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 906) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OC)cc1OC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000642042452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642042452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000642042452 none CCN(Cc1ccc(OC)cc1OC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 4, 4, 3, 4, 8, 4, 4, 4, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 4, 7, 7, 7, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 50 rigid atoms, others: [1, 2, 3, 14, 15, 16, 17, 18] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 64 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 907) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OC)cc1OC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000642042452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642042452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000642042452 none CCN(Cc1ccc(OC)cc1OC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 4, 4, 4, 4, 8, 4, 4, 4, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 4, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [1, 2, 3, 14, 15, 16, 17, 18] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 55 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642042452 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 Building ZINC000642042452 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642042452 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 906) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OC)cc1OC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000642042452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642042452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000642042452 none CCN(Cc1ccc(OC)cc1OC)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 4, 4, 3, 4, 8, 4, 4, 4, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 4, 7, 7, 7, 2, 2, 2, 10, 10, 4, 10, 2, 2, 2] 50 rigid atoms, others: [1, 2, 3, 14, 15, 16, 17, 18] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 64 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 907) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(Cc1ccc(OC)cc1OC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C) `ZINC000642042452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642042452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 64 natoms 63 natoms 62 natoms 61 names: ZINC000642042452 none CCN(Cc1ccc(OC)cc1OC)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 1, 1, 1, 1, 12, 5, 1, 1, 12, 5, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 2, 4, 4, 4, 4, 8, 4, 4, 4, 7, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 2, 10, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 8, 8, 8, 4, 7, 7, 7, 2, 2, 2, 10, 10, 2, 10, 2, 2, 2] 50 rigid atoms, others: [1, 2, 3, 14, 15, 16, 17, 18] set([0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 55 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642042452 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642042452 Building ZINC000642074571 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642074571 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 908) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccc(OC)c(OC)c1) `ZINC000642074571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642074571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642074571 none CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 11, 6, 6, 11, 6, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 6, 6, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 909) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccc(OC)c(OC)c1) `ZINC000642074571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642074571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642074571 none CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 11, 6, 6, 11, 6, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 6, 6, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642074571 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 Building ZINC000642074571 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642074571 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 908) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccc(OC)c(OC)c1) `ZINC000642074571.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642074571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642074571 none CCN(C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 11, 6, 6, 11, 6, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 2, 8, 2, 2, 2, 6, 6, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 909) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccc(OC)c(OC)c1) `ZINC000642074571.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642074571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642074571 none CCN(C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2cccc(C(F)(F)F)c2)c1C)c1ccc(OC)c(OC)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', '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'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 1, 1, 1, 12, 5, 1, 12, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 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, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 8, 8, 2, 8, 8, 8, 8, 8, 8, 2, 2, 2, 6, 6, 6, 6, 11, 6, 6, 11, 6, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 4, 8, 2, 2, 2, 6, 6, 11, 11, 11, 11, 11, 11, 6] 50 rigid atoms, others: [2, 3, 4, 5, 6, 7] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642074571 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642074571 Building ZINC000642143985 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642143985 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 910) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1n1cncn1) `ZINC000642143985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642143985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642143985 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 8, 8, 8, 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 911) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1n1cncn1) `ZINC000642143985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642143985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642143985 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 6, 6, 6, 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642143985 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 Building ZINC000642143985 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642143985 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 910) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1n1cncn1) `ZINC000642143985.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642143985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642143985 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 8, 8, 13, 13, 13, 13, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 4, 8, 8, 8, 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: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 911) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1n1cncn1) `ZINC000642143985.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642143985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642143985 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(Cl)c1n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 16, 1, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 6, 6, 6, 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642143985 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642143985 Building ZINC000642156694 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642156694 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 912) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000642156694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642156694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156694 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](C(F)(F)F)C[C@H](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.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 4, 6, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 77 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 913) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000642156694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642156694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156694 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](C(F)(F)F)C[C@H](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.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 6, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642156694 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 Building ZINC000642156694 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642156694 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 912) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000642156694.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642156694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156694 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](C(F)(F)F)C[C@H](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.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 13, 13, 13, 13, 13, 4, 4, 4, 6, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 77 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 913) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000642156694.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642156694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156694 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](C(F)(F)F)C[C@H](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.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 1, 1, 1, 1, 6, 6, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 4, 4, 4, 13, 13, 4, 13, 13, 4, 4, 4, 6, 24, 24, 24, 24, 24, 24] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 96 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642156694 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156694 Building ZINC000642156695 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642156695 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 914) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000642156695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642156695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156695 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 93 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 915) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000642156695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642156695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156695 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 4, 37, 37, 37, 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, 51, 52]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642156695 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 Building ZINC000642156695 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642156695 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 914) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000642156695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642156695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156695 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 1, 1, 1, 1, 4, 4, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 4, 4, 4, 7, 7, 4, 7, 7, 4, 4, 4, 4, 33, 33, 33, 33, 33, 33, 33] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 93 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 915) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1) `ZINC000642156695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642156695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156695 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@@H](C(F)(F)F)C[C@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 9, 9, 4, 4, 1, 1, 1, 1, 4, 4, 9, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 9, 9, 7, 9, 9, 4, 4, 4, 4, 37, 37, 37, 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, 51, 52]) total number of confs: 108 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642156695 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156695 Building ZINC000642156696 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642156696 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 916) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1) `ZINC000642156696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642156696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156696 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 3, 34, 34, 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]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 917) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1) `ZINC000642156696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642156696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156696 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642156696 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 Building ZINC000642156696 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642156696 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 916) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1) `ZINC000642156696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642156696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156696 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)NC1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 1, 1, 1, 1, 3, 3, 8, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 8, 8, 4, 8, 8, 4, 4, 4, 3, 34, 34, 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]) total number of confs: 102 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 917) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1) `ZINC000642156696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642156696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000642156696 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)NC1C[C@H](C(F)(F)F)C[C@@H](C(F)(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 5, 7, 5, 15, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 3, 3, 3, 8, 8, 3, 8, 8, 3, 3, 3, 3, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 94 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642156696 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642156696 Building ZINC000642298668 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642298668 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 918) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C2(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CCCCCC2)no1) `ZINC000642298668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642298668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000642298668 none Cc1nc(C2(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CCCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 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, 5, 5, 5, 5, 8, 12, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 13, 13, 13, 13, 4, 4, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 2, 4, 4, 4, 13, 13, 4, 13, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 919) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C2(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CCCCCC2)no1) `ZINC000642298668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642298668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000642298668 none Cc1nc(C2(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CCCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 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, 5, 5, 5, 5, 8, 12, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 13, 13, 13, 13, 4, 4, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 2, 4, 4, 4, 13, 13, 7, 13, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 60 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642298668 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 Building ZINC000642298668 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642298668 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 918) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C2(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CCCCCC2)no1) `ZINC000642298668.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642298668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000642298668 none Cc1nc(C2(NC(=O)[C@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CCCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 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, 5, 5, 5, 5, 8, 12, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 5, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 13, 13, 13, 13, 4, 4, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 11, 2, 4, 4, 4, 13, 13, 4, 13, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 919) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc(C2(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CCCCCC2)no1) `ZINC000642298668.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642298668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000642298668 none Cc1nc(C2(NC(=O)[C@@]([O-])([SiH3])c3c(C)nn(c4cccc(C(F)(F)F)c4)c3C)CCCCCC2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', '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', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 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, 5, 5, 5, 5, 8, 12, 7, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 3, 2, 1, 2, 1, 1, 1, 4, 4, 4, 4, 4, 13, 13, 4, 13, 13, 13, 13, 13, 13, 4, 4, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 10, 2, 4, 4, 4, 13, 13, 7, 13, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 50 rigid atoms, others: [8, 9, 10, 6] set([0, 1, 2, 3, 4, 5, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 60 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642298668 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642298668 Building ZINC000642299969 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642299969 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 920) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC000642299969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642299969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642299969 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 17, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 921) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC000642299969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642299969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642299969 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 30, 30, 13, 24, 30, 30, 30, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642299969 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 Building ZINC000642299969 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642299969 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 920) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC000642299969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642299969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642299969 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 1, 1, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 17, 17, 17, 35, 35, 35, 35, 35, 35, 35, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 17, 35, 35, 35] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 100 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 921) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC000642299969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642299969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642299969 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@H]1C(=O)Nc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 30, 30, 13, 24, 30, 30, 30, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 117 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642299969 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299969 Building ZINC000642299970 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642299970 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 922) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC000642299970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642299970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642299970 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 30, 30, 12, 24, 30, 30, 30, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 923) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC000642299970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642299970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642299970 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 34, 34, 16, 23, 34, 34, 34, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 16, 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]) total number of confs: 142 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642299970 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 Building ZINC000642299970 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642299970 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 922) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC000642299970.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642299970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642299970 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 30, 30, 12, 24, 30, 30, 30, 3, 3, 3, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 119 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 923) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl) `ZINC000642299970.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642299970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000642299970 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCCC[C@@H]1C(=O)Nc1ccc(Cl)cc1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 7, 1, 11, 8, 1, 1, 1, 1, 16, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 6, 6, 6, 6, 6, 6, 6, 16, 16, 16, 34, 34, 16, 23, 34, 34, 34, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 16, 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]) total number of confs: 142 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642299970 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642299970 Building ZINC000642518829 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642518829 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 924) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(n2cccn2)c1) `ZINC000642518829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642518829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642518829 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 1, 1, 8, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 925) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(n2cccn2)c1) `ZINC000642518829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642518829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642518829 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 1, 1, 8, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642518829 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 Building ZINC000642518829 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642518829 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 924) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(n2cccn2)c1) `ZINC000642518829.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642518829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642518829 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 1, 1, 8, 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, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 4, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 925) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(n2cccn2)c1) `ZINC000642518829.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642518829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000642518829 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(n2cccn2)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 1, 1, 1, 1, 8, 1, 1, 1, 8, 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, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 11, 11, 3, 11, 3, 3, 3, 3, 10, 10, 10, 10, 10, 10, 10] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642518829 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642518829 Building ZINC000642678263 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642678263 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 926) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1) `ZINC000642678263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642678263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000642678263 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 42, 47, 47, 47, 47, 11, 11, 11, 6, 2, 2, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 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/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 927) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1) `ZINC000642678263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642678263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000642678263 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 7, 7, 35, 42, 42, 42, 42, 15, 15, 15, 7, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642678263 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 Building ZINC000642678263 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642678263 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 926) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1) `ZINC000642678263.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642678263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000642678263 none COc1cc([C@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 42, 47, 47, 47, 47, 11, 11, 11, 6, 2, 2, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 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/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 927) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1) `ZINC000642678263.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642678263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000642678263 none COc1cc([C@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 7, 7, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 7, 7, 35, 42, 42, 42, 42, 15, 15, 15, 7, 3, 3, 3, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7, 42, 42, 42, 42, 42, 42, 42, 42, 42] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642678263 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678263 Building ZINC000642678264 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642678264 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 928) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1) `ZINC000642678264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642678264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000642678264 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 36, 46, 46, 46, 46, 13, 13, 13, 6, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 929) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1) `ZINC000642678264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642678264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000642678264 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 40, 48, 48, 48, 48, 12, 12, 12, 6, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642678264 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 Building ZINC000642678264 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000642678264 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 928) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1) `ZINC000642678264.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000642678264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000642678264 none COc1cc([C@@H](C)NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 6, 6, 3, 2, 3, 3, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 36, 46, 46, 46, 46, 13, 13, 13, 6, 3, 3, 3, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 6, 6, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 929) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1) `ZINC000642678264.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000642678264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 68 natoms 67 natoms 66 natoms 65 names: ZINC000642678264 none COc1cc([C@@H](C)NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)ccc1OC1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 6, 6, 6, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 6, 6, 6, 6, 40, 48, 48, 48, 48, 12, 12, 12, 6, 2, 2, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 6, 6, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000642678264 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000642678264 Building ZINC000643165976 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643165976 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 930) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)Nc1ccccc1n1cccn1) `ZINC000643165976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643165976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643165976 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 3, 3, 3, 12, 12, 7, 12, 3, 3, 3, 3, 5, 5, 5, 5, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 931) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)Nc1ccccc1n1cccn1) `ZINC000643165976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643165976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643165976 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 5, 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000643165976 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 Building ZINC000643165976 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643165976 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 930) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)Nc1ccccc1n1cccn1) `ZINC000643165976.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643165976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643165976 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 3, 3, 3, 12, 12, 7, 12, 3, 3, 3, 3, 5, 5, 5, 5, 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]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 931) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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)Nc1ccccc1n1cccn1) `ZINC000643165976.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643165976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643165976 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccccc1n1cccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 5, 10, 10, 10, 10, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 3, 5, 5, 5, 5, 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]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000643165976 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643165976 Building ZINC000643352192 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643352192 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 932) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2ccc(O)cc2)CC1) `ZINC000643352192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643352192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643352192 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 4, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 11, 11, 9, 9, 11, 11, 8, 8, 2, 2, 2, 14, 14, 8, 14, 2, 2, 2, 8, 8, 8, 8, 8, 11, 11, 22, 11, 11, 8, 8, 8, 8] 100 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: 91 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 933) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2ccc(O)cc2)CC1) `ZINC000643352192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643352192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643352192 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 4, 8, 9, 9, 9, 9, 14, 14, 9, 11, 14, 14, 9, 9, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 9, 9, 9, 9, 9, 14, 14, 28, 14, 14, 9, 9, 9, 9] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000643352192 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 Building ZINC000643352192 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643352192 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 932) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2ccc(O)cc2)CC1) `ZINC000643352192.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643352192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643352192 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 14, 14, 4, 14, 14, 14, 14, 14, 14, 2, 2, 1, 1, 1, 2, 4, 6, 8, 8, 8, 8, 11, 11, 9, 9, 11, 11, 8, 8, 2, 2, 2, 14, 14, 8, 14, 2, 2, 2, 8, 8, 8, 8, 8, 11, 11, 22, 11, 11, 8, 8, 8, 8] 100 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: 91 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 933) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(c2ccc(O)cc2)CC1) `ZINC000643352192.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643352192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643352192 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 11, 11, 2, 11, 11, 11, 11, 11, 11, 2, 2, 1, 1, 1, 1, 4, 8, 9, 9, 9, 9, 14, 14, 9, 11, 14, 14, 9, 9, 2, 2, 2, 11, 11, 2, 11, 2, 2, 2, 9, 9, 9, 9, 9, 14, 14, 28, 14, 14, 9, 9, 9, 9] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 91 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000643352192 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643352192 Building ZINC000643640262 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643640262 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 934) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(=O)c2ccc(O)cc2)CC1) `ZINC000643640262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643640262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643640262 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 11, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 12, 12, 24, 12, 12, 3, 3, 3, 3] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 935) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(=O)c2ccc(O)cc2)CC1) `ZINC000643640262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643640262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643640262 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 11, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 9, 9, 11, 11, 9, 11, 11, 11, 4, 4, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 11, 11, 22, 11, 11, 4, 4, 4, 4] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000643640262 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 Building ZINC000643640262 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000643640262 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 934) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(=O)c2ccc(O)cc2)CC1) `ZINC000643640262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000643640262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643640262 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 11, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 4, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 12, 12, 3, 3, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 3, 3, 3, 3, 3, 12, 12, 24, 12, 12, 3, 3, 3, 3] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 935) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(=O)c2ccc(O)cc2)CC1) `ZINC000643640262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000643640262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000643640262 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC(C(=O)c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 11, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 2, 4, 4, 4, 4, 4, 9, 9, 11, 11, 9, 11, 11, 11, 4, 4, 2, 2, 2, 8, 8, 8, 8, 2, 2, 2, 4, 4, 4, 4, 4, 11, 11, 22, 11, 11, 4, 4, 4, 4] 100 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000643640262 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000643640262 Building ZINC000644637688 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644637688 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 936) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)Nc2ccccc2)c1) `ZINC000644637688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644637688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000644637688 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)Nc2ccccc2)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', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 24, 24, 24, 26, 43, 43, 43, 43, 43, 12, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 12, 12, 12, 24, 26, 43, 43, 43, 43, 43, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 937) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)Nc2ccccc2)c1) `ZINC000644637688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644637688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000644637688 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)Nc2ccccc2)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', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 26, 26, 26, 27, 43, 43, 27, 43, 43, 13, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 3, 3, 13, 13, 13, 26, 27, 43, 43, 27, 43, 43, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000644637688 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 Building ZINC000644637688 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000644637688 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 936) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)Nc2ccccc2)c1) `ZINC000644637688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000644637688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000644637688 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)Nc2ccccc2)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', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 24, 24, 24, 26, 43, 43, 43, 43, 43, 12, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 12, 12, 12, 24, 26, 43, 43, 43, 43, 43, 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]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 937) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)Nc2ccccc2)c1) `ZINC000644637688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000644637688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000644637688 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(NC(=O)Nc2ccccc2)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', 'C.ar', 'N.am', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 8, 1, 11, 8, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 13, 13, 26, 26, 26, 27, 43, 43, 27, 43, 43, 13, 3, 3, 3, 6, 6, 4, 6, 6, 3, 3, 3, 3, 13, 13, 13, 26, 27, 43, 43, 27, 43, 43, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000644637688 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000644637688 Building ZINC000303005628 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303005628 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 938) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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(CC1CC1)c1ccc(Cl)c([N+](=O)[O-])c1) `ZINC000303005628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303005628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000303005628 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC1CC1)c1ccc(Cl)c([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 16, 1, 8, 11, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 9, 15, 15, 4, 17, 17, 4, 4, 17, 17, 17, 17, 17, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 9, 9, 15, 15, 15, 15, 15, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 939) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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(CC1CC1)c1ccc(Cl)c([N+](=O)[O-])c1) `ZINC000303005628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303005628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000303005628 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC1CC1)c1ccc(Cl)c([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 16, 1, 8, 11, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 5, 9, 18, 18, 5, 17, 17, 5, 9, 17, 17, 17, 17, 17, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 9, 9, 18, 18, 18, 18, 18, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303005628 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 Building ZINC000303005628 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000303005628 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 938) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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(CC1CC1)c1ccc(Cl)c([N+](=O)[O-])c1) `ZINC000303005628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000303005628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000303005628 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC1CC1)c1ccc(Cl)c([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 16, 1, 8, 11, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 9, 15, 15, 4, 17, 17, 4, 4, 17, 17, 17, 17, 17, 3, 3, 3, 8, 8, 5, 8, 8, 3, 3, 3, 9, 9, 15, 15, 15, 15, 15, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 118 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 939) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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(CC1CC1)c1ccc(Cl)c([N+](=O)[O-])c1) `ZINC000303005628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000303005628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000303005628 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC1CC1)c1ccc(Cl)c([N+](=O)[O-])c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'Cl', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] 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, 16, 1, 8, 11, 11, 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, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 3, 5, 9, 18, 18, 5, 17, 17, 5, 9, 17, 17, 17, 17, 17, 3, 3, 3, 10, 10, 3, 10, 10, 3, 3, 3, 9, 9, 18, 18, 18, 18, 18, 17, 17, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 129 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000303005628 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000303005628 Building ZINC000646078619 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000646078619 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 940) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1) `ZINC000646078619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000646078619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646078619 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@@H]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 8, 8, 8, 5, 13, 13, 13, 37, 37, 33, 34, 37, 37, 37, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 8, 8, 8, 8, 37, 37, 37, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 87 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 941) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1) `ZINC000646078619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000646078619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646078619 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@@H]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 8, 10, 10, 10, 10, 10, 3, 7, 7, 7, 28, 28, 13, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 10, 10, 10, 10, 28, 28, 28, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000646078619 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 Building ZINC000646078619 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000646078619 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 940) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1) `ZINC000646078619.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000646078619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646078619 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@@H]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 8, 8, 8, 5, 13, 13, 13, 37, 37, 33, 34, 37, 37, 37, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 8, 8, 8, 8, 37, 37, 37, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 87 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 941) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1) `ZINC000646078619.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000646078619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646078619 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@@H]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 8, 10, 10, 10, 10, 10, 3, 7, 7, 7, 28, 28, 13, 28, 28, 28, 28, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 10, 10, 10, 10, 28, 28, 28, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 126 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000646078619 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078619 Building ZINC000646078626 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000646078626 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 942) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1) `ZINC000646078626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000646078626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646078626 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 8, 10, 10, 10, 10, 10, 3, 8, 8, 8, 30, 30, 8, 20, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 10, 10, 10, 10, 30, 30, 30, 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]) total number of confs: 120 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 943) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1) `ZINC000646078626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000646078626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646078626 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 8, 8, 8, 5, 13, 13, 13, 37, 37, 35, 37, 37, 37, 37, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 8, 8, 8, 8, 37, 37, 37, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000646078626 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 Building ZINC000646078626 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000646078626 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 942) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1) `ZINC000646078626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000646078626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646078626 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 3, 8, 10, 10, 10, 10, 10, 3, 8, 8, 8, 30, 30, 8, 20, 30, 30, 30, 8, 8, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 6, 10, 10, 10, 10, 10, 10, 30, 30, 30, 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]) total number of confs: 120 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 943) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1) `ZINC000646078626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000646078626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000646078626 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@H]1CCCO1)c1nc(c2ccc(Cl)cc2Cl)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 16, 1, 1, 16, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 8, 8, 8, 5, 13, 13, 13, 37, 37, 35, 37, 37, 37, 37, 13, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 7, 7, 8, 8, 8, 8, 8, 8, 37, 37, 37, 13] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000646078626 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000646078626 Building ZINC000647555505 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647555505 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 944) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccc(OC)c(Cl)c2)cc1) `ZINC000647555505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647555505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000647555505 none CCOc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 13, 13, 7, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 8, 8, 13, 8, 8, 8, 13, 13, 21, 21, 21, 21, 21, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 13, 8, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 945) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccc(OC)c(Cl)c2)cc1) `ZINC000647555505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647555505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000647555505 none CCOc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 12, 13, 13, 7, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 8, 8, 13, 8, 8, 8, 13, 13, 20, 20, 20, 20, 20, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 13, 8, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000647555505 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 Building ZINC000647555505 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000647555505 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 944) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccc(OC)c(Cl)c2)cc1) `ZINC000647555505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000647555505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000647555505 none CCOc1ccc(CN(C(=O)[C@@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 13, 13, 7, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 8, 8, 13, 8, 8, 8, 13, 13, 21, 21, 21, 21, 21, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 13, 8, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 945) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccc(OC)c(Cl)c2)cc1) `ZINC000647555505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000647555505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 61 natoms 60 natoms 59 natoms 58 names: ZINC000647555505 none CCOc1ccc(CN(C(=O)[C@]([O-])([SiH3])c2c(C)nn(C)c2C)c2ccc(OC)c(Cl)c2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 5, 1, 1, 1, 1, 12, 5, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 12, 13, 13, 7, 4, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 4, 8, 8, 8, 8, 13, 8, 8, 8, 13, 13, 20, 20, 20, 20, 20, 13, 13, 7, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 8, 8, 13, 13, 13, 8, 13, 13] 50 rigid atoms, others: [9, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 78 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000647555505 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000647555505 Building ZINC000648037761 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648037761 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 946) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648037761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648037761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000648037761 none COc1ccccc1NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 22, 22, 11, 11, 7, 11, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 31, 31, 31, 22, 22, 22, 22, 11, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 947) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648037761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648037761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000648037761 none COc1ccccc1NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 24, 24, 12, 24, 24, 12, 12, 6, 12, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 32, 32, 32, 24, 24, 24, 24, 12, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000648037761 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 Building ZINC000648037761 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648037761 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 946) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648037761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648037761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000648037761 none COc1ccccc1NC(=O)c1ccc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 22, 22, 11, 11, 7, 11, 6, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 7, 7, 31, 31, 31, 22, 22, 22, 22, 11, 7, 7, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 7, 7] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 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/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 947) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1) `ZINC000648037761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648037761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC000648037761 none COc1ccccc1NC(=O)c1ccc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)cc1 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.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 24, 24, 12, 24, 24, 12, 12, 6, 12, 6, 8, 8, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 32, 32, 32, 24, 24, 24, 24, 12, 8, 8, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 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]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000648037761 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648037761 Building ZINC000648099175 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648099175 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 948) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(Cc1ccco1)CC(F)(F)F) `ZINC000648099175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648099175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648099175 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 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, 3, 6, 10, 10, 10, 10, 3, 5, 5, 5, 5, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 6, 6, 10, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 949) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(Cc1ccco1)CC(F)(F)F) `ZINC000648099175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648099175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648099175 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 3, 6, 10, 10, 10, 10, 3, 5, 5, 5, 5, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 6, 6, 10, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000648099175 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 Building ZINC000648099175 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648099175 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 948) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(Cc1ccco1)CC(F)(F)F) `ZINC000648099175.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648099175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648099175 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(Cc1ccco1)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 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, 3, 6, 10, 10, 10, 10, 3, 5, 5, 5, 5, 3, 3, 3, 14, 14, 3, 14, 3, 3, 3, 6, 6, 10, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 71 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 949) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(Cc1ccco1)CC(F)(F)F) `ZINC000648099175.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648099175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648099175 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(Cc1ccco1)CC(F)(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'F', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 12, 5, 5, 15, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 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, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 2, 2, 3, 6, 10, 10, 10, 10, 3, 5, 5, 5, 5, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 6, 6, 10, 10, 10, 5, 5] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 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: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000648099175 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648099175 Building ZINC000648452670 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648452670 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 950) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(c2ccccc2)nc1) `ZINC000648452670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648452670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648452670 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(c2ccccc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 4, 4, 11, 11, 4, 11, 11, 6, 6, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 6, 11, 11, 4, 11, 11, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 951) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(c2ccccc2)nc1) `ZINC000648452670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648452670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648452670 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(c2ccccc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 4, 4, 4, 6, 6, 4, 4, 12, 12, 4, 12, 12, 6, 6, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 4, 6, 12, 12, 4, 12, 12, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 87 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000648452670 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 Building ZINC000648452670 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648452670 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 950) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(c2ccccc2)nc1) `ZINC000648452670.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648452670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648452670 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cnc(c2ccccc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 25, 25, 4, 25, 25, 25, 25, 25, 25, 4, 4, 1, 1, 1, 1, 4, 4, 4, 6, 6, 4, 4, 11, 11, 4, 11, 11, 6, 6, 4, 4, 4, 25, 25, 4, 25, 4, 4, 4, 4, 6, 11, 11, 4, 11, 11, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 97 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 951) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(c2ccccc2)nc1) `ZINC000648452670.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648452670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000648452670 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cnc(c2ccccc2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 8, 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, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 20, 20, 3, 20, 20, 20, 20, 20, 20, 3, 3, 1, 1, 1, 1, 4, 4, 4, 6, 6, 4, 4, 12, 12, 4, 12, 12, 6, 6, 3, 3, 3, 20, 20, 3, 20, 3, 3, 3, 4, 6, 12, 12, 4, 12, 12, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 87 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000648452670 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648452670 Building ZINC000648523774 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648523774 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 952) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C)nn(c3ccccc3)c2C)n(c2ccccc2C(F)(F)F)n1) `ZINC000648523774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648523774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000648523774 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2ccccc2C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 10, 10, 26, 26, 19, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 5, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 26, 26, 19, 26] 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 953) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C)nn(c3ccccc3)c2C)n(c2ccccc2C(F)(F)F)n1) `ZINC000648523774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648523774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000648523774 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2ccccc2C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 10, 10, 26, 26, 19, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 26, 26, 19, 26] 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000648523774 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 Building ZINC000648523774 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000648523774 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 952) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C)nn(c3ccccc3)c2C)n(c2ccccc2C(F)(F)F)n1) `ZINC000648523774.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000648523774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000648523774 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2ccccc2C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 10, 10, 26, 26, 19, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 5, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2, 26, 26, 19, 26] 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: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 953) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(C)nn(c3ccccc3)c2C)n(c2ccccc2C(F)(F)F)n1) `ZINC000648523774.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000648523774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC000648523774 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2c(C)nn(c3ccccc3)c2C)n(c2ccccc2C(F)(F)F)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 10, 10, 26, 26, 19, 26, 26, 26, 26, 26, 26, 10, 10, 10, 10, 10, 5, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2, 26, 26, 19, 26] 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: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000648523774 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000648523774 Building ZINC000649235038 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649235038 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 954) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1) `ZINC000649235038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649235038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000649235038 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 7, 10, 10, 10, 10, 10, 4, 7, 7, 7, 43, 43, 7, 43, 43, 43, 43, 43, 43, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 10, 10, 10, 10, 10, 10, 43, 43, 13, 43, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 955) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1) `ZINC000649235038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649235038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000649235038 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 10, 10, 2, 6, 6, 6, 35, 35, 6, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 10, 10, 10, 35, 35, 6, 35, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000649235038 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 Building ZINC000649235038 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000649235038 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 954) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1) `ZINC000649235038.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000649235038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000649235038 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N(C[C@@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 3, 4, 7, 10, 10, 10, 10, 10, 4, 7, 7, 7, 43, 43, 7, 43, 43, 43, 43, 43, 43, 7, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 10, 10, 10, 10, 10, 10, 43, 43, 13, 43, 7] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 140 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 955) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1) `ZINC000649235038.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000649235038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC000649235038 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N(C[C@@H]1CCCO1)c1nc(c2cccc(C(F)(F)F)c2)cs1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 12, 1, 8, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 6, 10, 10, 10, 10, 10, 2, 6, 6, 6, 35, 35, 6, 35, 35, 35, 35, 35, 35, 6, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 10, 10, 10, 10, 10, 10, 35, 35, 6, 35, 6] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000649235038 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000649235038 Building ZINC000650657172 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650657172 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 956) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000650657172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650657172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000650657172 none COc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 6, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 18, 18, 18, 12, 12, 3, 4, 4, 4, 10, 10, 4, 10, 10, 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]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 957) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000650657172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650657172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000650657172 none COc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 3, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 19, 19, 19, 12, 12, 3, 4, 4, 4, 9, 9, 8, 9, 9, 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000650657172 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 Building ZINC000650657172 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000650657172 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 956) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000650657172.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000650657172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000650657172 none COc1c(Br)cc(Cl)cc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 6, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 18, 18, 18, 12, 12, 3, 4, 4, 4, 10, 10, 4, 10, 10, 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]) total number of confs: 80 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 957) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000650657172.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000650657172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC000650657172 none COc1c(Br)cc(Cl)cc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', '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'] dock atom type numbers: [5, 12, 1, 1, 17, 1, 1, 16, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 12, 12, 12, 3, 12, 12, 12, 3, 3, 1, 3, 1, 1, 1, 4, 4, 4, 4, 4, 9, 9, 5, 9, 9, 4, 4, 19, 19, 19, 12, 12, 3, 4, 4, 4, 9, 9, 8, 9, 9, 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]) total number of confs: 89 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000650657172 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000650657172 Building ZINC000748661998 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748661998 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 958) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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(N2CCSCC2)c(Cl)c1) `ZINC000748661998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748661998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000748661998 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCSCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 17, 17, 14, 26, 39, 39, 39, 39, 39, 17, 17, 17, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 959) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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(N2CCSCC2)c(Cl)c1) `ZINC000748661998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748661998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000748661998 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCSCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 22, 32, 32, 32, 32, 32, 13, 13, 13, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000748661998 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 Building ZINC000748661998 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000748661998 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 958) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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(N2CCSCC2)c(Cl)c1) `ZINC000748661998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000748661998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000748661998 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCSCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 4, 4, 4, 17, 17, 14, 26, 39, 39, 39, 39, 39, 17, 17, 17, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 4, 17, 17, 39, 39, 39, 39, 39, 39, 39, 39, 17] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 959) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.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(N2CCSCC2)c(Cl)c1) `ZINC000748661998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000748661998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC000748661998 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCSCC2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'S.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 14, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 1, 1, 1, 1, 3, 3, 3, 13, 13, 13, 22, 32, 32, 32, 32, 32, 13, 13, 13, 3, 3, 3, 6, 6, 3, 6, 6, 3, 3, 3, 3, 13, 13, 32, 32, 32, 32, 32, 32, 32, 32, 13] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 72 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000748661998 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000748661998 Building ZINC000749139594 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749139594 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 960) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(n2cncn2)c(Cl)c1) `ZINC000749139594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749139594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000749139594 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2cncn2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 13, 13, 13, 13, 8, 8, 8, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 2, 8, 8, 13, 13, 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]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 961) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(n2cncn2)c(Cl)c1) `ZINC000749139594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749139594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000749139594 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2cncn2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 13, 13, 13, 13, 8, 8, 8, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 3, 8, 8, 13, 13, 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]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000749139594 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 Building ZINC000749139594 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000749139594 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 960) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(n2cncn2)c(Cl)c1) `ZINC000749139594.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000749139594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000749139594 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(n2cncn2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 13, 13, 13, 13, 8, 8, 8, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 2, 8, 8, 13, 13, 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]) total number of confs: 59 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 961) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(n2cncn2)c(Cl)c1) `ZINC000749139594.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000749139594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000749139594 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(n2cncn2)c(Cl)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', '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, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 1, 8, 1, 8, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 13, 13, 3, 13, 13, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 13, 13, 13, 13, 8, 8, 8, 3, 3, 3, 13, 13, 3, 13, 3, 3, 3, 3, 8, 8, 13, 13, 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]) total number of confs: 55 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000749139594 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000749139594 Building ZINC000678999211 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000678999211 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 962) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)Nc1cc(Cl)ccc1Cl)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000678999211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000678999211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000678999211 none CCCN(CC(=O)Nc1cc(Cl)ccc1Cl)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 3, 2, 3, 3, 6, 6, 6, 18, 18, 18, 14, 18, 18, 18, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 8, 8, 8, 7, 7, 3, 3, 6, 18, 18, 18, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 963) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)Nc1cc(Cl)ccc1Cl)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000678999211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000678999211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000678999211 none CCCN(CC(=O)Nc1cc(Cl)ccc1Cl)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 3, 2, 3, 5, 10, 10, 10, 26, 26, 26, 21, 26, 26, 26, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 8, 8, 8, 8, 8, 7, 7, 5, 5, 10, 26, 26, 26, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000678999211 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 Building ZINC000678999211 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000678999211 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 962) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)Nc1cc(Cl)ccc1Cl)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000678999211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000678999211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000678999211 none CCCN(CC(=O)Nc1cc(Cl)ccc1Cl)C(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 3, 2, 3, 3, 6, 6, 6, 18, 18, 18, 14, 18, 18, 18, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 8, 8, 8, 8, 8, 7, 7, 3, 3, 6, 18, 18, 18, 2, 2, 2, 4, 4, 4, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 87 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 963) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CC(=O)Nc1cc(Cl)ccc1Cl)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC000678999211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000678999211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC000678999211 none CCCN(CC(=O)Nc1cc(Cl)ccc1Cl)C(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C 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', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 1, 11, 8, 1, 1, 1, 16, 1, 1, 1, 16, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 3, 2, 3, 5, 10, 10, 10, 26, 26, 26, 21, 26, 26, 26, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 8, 8, 8, 8, 8, 7, 7, 5, 5, 10, 26, 26, 26, 2, 2, 2, 4, 4, 2, 4, 4, 2, 2, 2] 50 rigid atoms, others: [16, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 121 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000678999211 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000678999211 Building ZINC000680686080 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680686080 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 964) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(OC(F)F)cc1) `ZINC000680686080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680686080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000680686080 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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, 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, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 16, 16, 4, 4, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 4, 4, 16, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 965) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(OC(F)F)cc1) `ZINC000680686080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680686080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000680686080 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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, 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, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 4, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 16, 17, 17, 4, 4, 3, 3, 3, 10, 10, 6, 10, 3, 3, 3, 2, 4, 4, 17, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000680686080 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 Building ZINC000680686080 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680686080 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 964) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(OC(F)F)cc1) `ZINC000680686080.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680686080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000680686080 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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, 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, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 9, 9, 3, 9, 9, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 15, 16, 16, 4, 4, 3, 3, 3, 9, 9, 3, 9, 3, 3, 3, 2, 4, 4, 16, 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]) total number of confs: 51 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 965) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(OC(F)F)cc1) `ZINC000680686080.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680686080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000680686080 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(OC(F)F)cc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'F', '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, 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, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 10, 10, 4, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 16, 17, 17, 4, 4, 3, 3, 3, 10, 10, 6, 10, 3, 3, 3, 2, 4, 4, 17, 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000680686080 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680686080 Building ZINC000680816479 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680816479 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 966) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(O)cc2)CC1) `ZINC000680816479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680816479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680816479 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 12, 12, 7, 8, 12, 12, 6, 6, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 6, 6, 6, 12, 12, 24, 12, 12, 6, 6, 6, 6] 100 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 967) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(O)cc2)CC1) `ZINC000680816479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680816479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680816479 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 12, 12, 9, 9, 12, 12, 6, 6, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 6, 6, 6, 12, 12, 24, 12, 12, 6, 6, 6, 6] 100 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000680816479 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 Building ZINC000680816479 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000680816479 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 966) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(O)cc2)CC1) `ZINC000680816479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000680816479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680816479 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 12, 12, 7, 8, 12, 12, 6, 6, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 6, 6, 6, 12, 12, 24, 12, 12, 6, 6, 6, 6] 100 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 93 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 967) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(O)cc2)CC1) `ZINC000680816479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000680816479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC000680816479 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC=C(c2ccc(O)cc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 12, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 16, 16, 2, 16, 16, 16, 16, 16, 16, 2, 2, 1, 1, 1, 2, 4, 6, 6, 6, 6, 6, 12, 12, 9, 9, 12, 12, 6, 6, 2, 2, 2, 16, 16, 2, 16, 2, 2, 2, 6, 6, 6, 12, 12, 24, 12, 12, 6, 6, 6, 6] 100 rigid atoms, others: [16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 89 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000680816479 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000680816479 Building ZINC000726148357 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726148357 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 968) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(F)(F)F)n1) `ZINC000726148357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726148357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000726148357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(F)(F)F)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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 6, 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]) total number of confs: 73 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 969) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(F)(F)F)n1) `ZINC000726148357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726148357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000726148357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(F)(F)F)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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 23, 23, 6, 23, 4, 4, 4, 6, 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]) total number of confs: 75 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000726148357 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 Building ZINC000726148357 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726148357 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 968) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(F)(F)F)n1) `ZINC000726148357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726148357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000726148357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cccc(C(F)(F)F)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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 24, 24, 4, 24, 24, 24, 24, 24, 24, 4, 4, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 24, 24, 4, 24, 4, 4, 4, 6, 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]) total number of confs: 73 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 969) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(F)(F)F)n1) `ZINC000726148357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726148357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000726148357 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cccc(C(F)(F)F)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.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 23, 23, 4, 23, 23, 23, 23, 23, 23, 4, 4, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 4, 4, 23, 23, 6, 23, 4, 4, 4, 6, 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]) total number of confs: 75 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000726148357 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726148357 Building ZINC000726509085 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726509085 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 970) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCN2C(=O)OC(C)(C)C) `ZINC000726509085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726509085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000726509085 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 31, 31, 31, 31, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 3, 15, 15, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 971) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCN2C(=O)OC(C)(C)C) `ZINC000726509085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726509085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000726509085 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 5, 10, 10, 4, 4, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 25, 25, 30, 30, 30, 30, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000726509085 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 Building ZINC000726509085 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000726509085 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 970) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCN2C(=O)OC(C)(C)C) `ZINC000726509085.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000726509085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000726509085 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 1, 1, 1, 1, 3, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 15, 26, 26, 31, 31, 31, 31, 4, 4, 4, 9, 9, 4, 9, 9, 4, 4, 4, 3, 15, 15, 15, 15, 15, 15, 15, 31, 31, 31, 31, 31, 31, 31, 31, 31] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 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/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 971) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCN2C(=O)OC(C)(C)C) `ZINC000726509085.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000726509085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 65 natoms 64 natoms 63 natoms 62 names: ZINC000726509085 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc2c(c1)CCN2C(=O)OC(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 1, 1, 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] 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, 6, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 10, 10, 5, 10, 10, 4, 4, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 25, 25, 30, 30, 30, 30, 4, 4, 4, 10, 10, 4, 10, 10, 4, 4, 4, 4, 16, 16, 16, 16, 16, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 30] 50 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) total number of confs: 85 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000726509085 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000726509085 Building ZINC000751072989 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751072989 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 972) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2sc(c3ccc(N(C(=O)[C@@]([O-])([SiH3])c4cnn(C)c4)C4=NCCCS4)cc3)nc2c1) `ZINC000751072989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751072989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000751072989 none Cc1ccc2sc(c3ccc(N(C(=O)[C@@]([O-])([SiH3])c4cnn(C)c4)C4=NCCCS4)cc3)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 14, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 14, 10, 16, 16, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 6, 12, 12, 12, 12, 10, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 16, 16, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 973) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2sc(c3ccc(N(C(=O)[C@]([O-])([SiH3])c4cnn(C)c4)C4=NCCCS4)cc3)nc2c1) `ZINC000751072989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751072989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000751072989 none Cc1ccc2sc(c3ccc(N(C(=O)[C@]([O-])([SiH3])c4cnn(C)c4)C4=NCCCS4)cc3)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 14, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 16, 8, 16, 16, 4, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 4, 11, 11, 11, 11, 8, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 16, 16, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 16, 16, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000751072989 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 Building ZINC000751072989 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751072989 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 972) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2sc(c3ccc(N(C(=O)[C@@]([O-])([SiH3])c4cnn(C)c4)C4=NCCCS4)cc3)nc2c1) `ZINC000751072989.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751072989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000751072989 none Cc1ccc2sc(c3ccc(N(C(=O)[C@@]([O-])([SiH3])c4cnn(C)c4)C4=NCCCS4)cc3)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 14, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 14, 10, 16, 16, 6, 5, 1, 5, 1, 1, 1, 8, 8, 8, 8, 8, 6, 12, 12, 12, 12, 10, 16, 16, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 8, 8, 8, 8, 8, 12, 12, 12, 12, 12, 12, 16, 16, 23] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 973) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ccc2sc(c3ccc(N(C(=O)[C@]([O-])([SiH3])c4cnn(C)c4)C4=NCCCS4)cc3)nc2c1) `ZINC000751072989.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751072989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC000751072989 none Cc1ccc2sc(c3ccc(N(C(=O)[C@]([O-])([SiH3])c4cnn(C)c4)C4=NCCCS4)cc3)nc2c1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 14, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 1, 8, 5, 5, 5, 14, 1, 1, 8, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 16, 8, 16, 16, 4, 3, 1, 3, 1, 1, 1, 8, 8, 8, 8, 8, 4, 11, 11, 11, 11, 8, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 16, 16, 8, 8, 8, 8, 8, 11, 11, 11, 11, 11, 11, 16, 16, 24] 50 rigid atoms, others: [16, 12, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000751072989 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751072989 Building ZINC000751106523 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751106523 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 974) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)c1ccccn1) `ZINC000751106523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751106523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000751106523 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 15, 15, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 6, 8, 8, 8, 8, 6, 11, 11, 11, 11, 11, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3, 8, 8, 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]) total number of confs: 74 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 975) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)c1ccccn1) `ZINC000751106523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751106523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000751106523 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 15, 15, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 4, 4, 6, 8, 8, 8, 8, 6, 10, 10, 10, 10, 10, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 8, 8, 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]) total number of confs: 71 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000751106523 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 Building ZINC000751106523 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000751106523 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 974) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)c1ccccn1) `ZINC000751106523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000751106523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000751106523 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)N(CC(F)(F)F)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 15, 15, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 4, 4, 6, 8, 8, 8, 8, 6, 11, 11, 11, 11, 11, 3, 3, 3, 14, 14, 6, 14, 3, 3, 3, 8, 8, 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]) total number of confs: 74 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 975) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)c1ccccn1) `ZINC000751106523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000751106523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000751106523 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)N(CC(F)(F)F)c1ccccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.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', 'F', 'F', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type 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, 15, 15, 15, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in 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, 3, 16, 16, 16, 16, 16, 16, 3, 3, 1, 1, 1, 1, 4, 4, 6, 8, 8, 8, 8, 6, 10, 10, 10, 10, 10, 3, 3, 3, 16, 16, 3, 16, 3, 3, 3, 8, 8, 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]) total number of confs: 71 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000751106523 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000751106523 Building ZINC000798986267 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000798986267 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 976) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2s1) `ZINC000798986267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000798986267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000798986267 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 5, 9, 18, 18, 18] 39 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 977) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2s1) `ZINC000798986267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000798986267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000798986267 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 15, 15, 11, 15, 15, 6, 6, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 15, 15, 13, 15, 15, 6, 6, 6, 9, 18, 18, 18] 46 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000798986267 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 Building ZINC000798986267 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000798986267 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 976) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2s1) `ZINC000798986267.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000798986267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000798986267 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 13, 13, 5, 13, 13, 5, 5, 5, 9, 18, 18, 18] 39 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 73 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 977) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2s1) `ZINC000798986267.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000798986267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 46 natoms 45 natoms 44 natoms 43 names: ZINC000798986267 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1nc2ccc(Br)cc2s1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 8, 1, 1, 1, 1, 17, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 15, 15, 11, 15, 15, 6, 6, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 6, 15, 15, 13, 15, 15, 6, 6, 6, 9, 18, 18, 18] 46 rigid atoms, others: [12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000798986267 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000798986267 Building ZINC000011749051 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011749051 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 978) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(N2CCCC2=O)c(C)c1) `ZINC000011749051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011749051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000011749051 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2=O)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 2, 11, 11, 11, 11, 11, 6, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 979) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(N2CCCC2=O)c(C)c1) `ZINC000011749051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011749051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000011749051 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2=O)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 3, 11, 11, 11, 11, 11, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000011749051 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 Building ZINC000011749051 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000011749051 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 978) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(N2CCCC2=O)c(C)c1) `ZINC000011749051.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000011749051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000011749051 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2=O)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 6, 6, 2, 2, 11, 11, 11, 11, 11, 6, 6, 6, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 6, 6, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 979) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d 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(N2CCCC2=O)c(C)c1) `ZINC000011749051.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000011749051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC000011749051 none Cc1nn(c2cccc(C(F)(F)F)c2)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1ccc(N2CCCC2=O)c(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 1, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 12, 12, 3, 12, 12, 12, 12, 12, 12, 3, 3, 1, 1, 1, 1, 2, 2, 2, 8, 8, 2, 3, 11, 11, 11, 11, 11, 8, 8, 8, 3, 3, 3, 12, 12, 3, 12, 3, 3, 3, 2, 8, 8, 11, 11, 11, 11, 11, 11, 8, 8, 8, 8] 50 rigid atoms, others: [16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000011749051 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000011749051 Building ZINC000831844055 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000831844055 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 980) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(Br)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000831844055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000831844055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000831844055 none CCOC(=O)c1c(c2ccc(Br)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 3, 7, 5, 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: [41, 33, 33, 7, 33, 7, 7, 7, 15, 15, 7, 11, 15, 15, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 15, 15, 15, 15, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 981) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(Br)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000831844055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000831844055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000831844055 none CCOC(=O)c1c(c2ccc(Br)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 3, 7, 5, 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: [41, 33, 32, 7, 32, 7, 7, 7, 14, 14, 10, 14, 14, 14, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 14, 14, 14, 14, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000831844055 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 Building ZINC000831844055 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC000831844055 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 980) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(Br)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000831844055.mol2' -> `0.mol2' `temp.mol2' -> `ZINC000831844055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000831844055 none CCOC(=O)c1c(c2ccc(Br)cc2)csc1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 3, 7, 5, 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: [41, 33, 33, 7, 33, 7, 7, 7, 15, 15, 7, 11, 15, 15, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 15, 15, 15, 15, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 154 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 981) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC(=O)c1c(c2ccc(Br)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C) `ZINC000831844055.mol2' -> `1.mol2' `temp.mol2' -> `ZINC000831844055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC000831844055 none CCOC(=O)c1c(c2ccc(Br)cc2)csc1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(C)c1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'S.3', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 17, 1, 1, 1, 14, 1, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 5, 1, 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, 3, 7, 5, 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: [41, 33, 32, 7, 32, 7, 7, 7, 14, 14, 10, 14, 14, 14, 7, 7, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 41, 41, 41, 41, 41, 14, 14, 14, 14, 7, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [18, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC000831844055 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC000831844055 Building ZINC001142279027 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279027 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 982) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc(OC)c1OC) `ZINC001142279027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001142279027 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 8, 11, 2, 4, 11, 11, 11, 11, 8, 2, 8, 8, 8, 16, 8, 2, 1, 3, 3, 3, 8, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 983) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])c2ccco2)cc(OC)c1OC) `ZINC001142279027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001142279027 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])c2ccco2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 8, 11, 4, 4, 11, 11, 11, 11, 8, 2, 8, 8, 8, 16, 8, 2, 1, 3, 3, 3, 8, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142279027 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 Building ZINC001142279027 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142279027 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 982) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc(OC)c1OC) `ZINC001142279027.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142279027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001142279027 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 8, 11, 2, 4, 11, 11, 11, 11, 8, 2, 8, 8, 8, 16, 8, 2, 1, 3, 3, 3, 8, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 983) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])c2ccco2)cc(OC)c1OC) `ZINC001142279027.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142279027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 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: ZINC001142279027 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])c2ccco2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [11, 8, 8, 8, 2, 2, 2, 2, 2, 8, 8, 8, 8, 8, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 8, 8, 11, 4, 4, 11, 11, 11, 11, 8, 2, 8, 8, 8, 16, 8, 2, 1, 3, 3, 3, 8, 11, 11, 11, 11, 11, 11] 100 rigid atoms, others: [46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 70 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142279027 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142279027 Building ZINC001142285946 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142285946 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 984) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccco2)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21) `ZINC001142285946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142285946 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 11, 11, 2, 4, 27, 36, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 11, 11, 11, 11, 2, 3, 3, 3, 11, 11, 45, 44, 44, 44, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 985) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccco2)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21) `ZINC001142285946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142285946 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 17, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 11, 11, 11, 11, 2, 5, 5, 5, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142285946 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 Building ZINC001142285946 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142285946 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 984) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccco2)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21) `ZINC001142285946.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142285946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142285946 none Cc1cc(NC(=O)[C@@]([O-])([SiH3])c2ccco2)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 11, 11, 2, 4, 27, 36, 44, 44, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 11, 11, 11, 11, 2, 3, 3, 3, 11, 11, 45, 44, 44, 44, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 121 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 985) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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])c2ccco2)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21) `ZINC001142285946.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142285946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001142285946 none Cc1cc(NC(=O)[C@]([O-])([SiH3])c2ccco2)ccc1C(=O)N1CCCC(=O)c2cc(Cl)ccc21 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 1, 11, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 17, 40, 40, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 11, 11, 11, 11, 2, 5, 5, 5, 11, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142285946 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142285946 Building ZINC001142286165 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286165 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 986) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1)c1cccnc1) `ZINC001142286165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142286165 none COC(=O)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [40, 40, 40, 40, 21, 6, 6, 18, 18, 6, 6, 6, 5, 5, 5, 3, 5, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 18, 18, 40, 50, 50, 50, 50, 50, 40, 40, 40, 21, 21, 18, 18, 6, 5, 5, 5, 5, 3, 3, 3, 3, 18, 18, 50, 50, 50, 50] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 987) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1)c1cccnc1) `ZINC001142286165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142286165 none COC(=O)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 20, 17, 17, 17, 17, 5, 5, 5, 4, 4, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 17, 17, 39, 50, 50, 50, 50, 50, 39, 39, 39, 20, 20, 17, 17, 5, 4, 4, 4, 4, 2, 3, 3, 3, 17, 17, 50, 50, 50, 50] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142286165 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 Building ZINC001142286165 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142286165 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 986) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1)c1cccnc1) `ZINC001142286165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142286165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142286165 none COC(=O)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@@]([O-])([SiH3])c2ccco2)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 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: [40, 40, 40, 40, 21, 6, 6, 18, 18, 6, 6, 6, 5, 5, 5, 3, 5, 5, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 3, 18, 18, 40, 50, 50, 50, 50, 50, 40, 40, 40, 21, 21, 18, 18, 6, 5, 5, 5, 5, 3, 3, 3, 3, 18, 18, 50, 50, 50, 50] 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]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 987) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1)c1cccnc1) `ZINC001142286165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142286165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 62 natoms 61 natoms 60 natoms 59 names: ZINC001142286165 none COC(=O)N(Cc1ccc(C(=O)Nc2ccccc2NC(=O)[C@]([O-])([SiH3])c2ccco2)cc1)c1cccnc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', '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.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 8, 1, 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, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 20, 17, 17, 17, 17, 5, 5, 5, 4, 4, 4, 2, 4, 4, 2, 2, 1, 2, 1, 1, 1, 3, 3, 3, 3, 17, 17, 39, 50, 50, 50, 50, 50, 39, 39, 39, 20, 20, 17, 17, 5, 4, 4, 4, 4, 2, 3, 3, 3, 17, 17, 50, 50, 50, 50] 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]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142286165 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142286165 Building ZINC001142290758 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142290758 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 988) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Cc2cccc(C(F)(F)F)c2)(NC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142290758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142290758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001142290758 none CC(C)(C)OC(=O)N1CCC(Cc2cccc(C(F)(F)F)c2)(NC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 15, 10, 15, 10, 10, 10, 6, 10, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 19, 19, 30, 30, 30, 30, 4, 6, 6, 6, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 989) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Cc2cccc(C(F)(F)F)c2)(NC(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142290758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142290758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001142290758 none CC(C)(C)OC(=O)N1CCC(Cc2cccc(C(F)(F)F)c2)(NC(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 16, 11, 11, 11, 6, 10, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 20, 20, 30, 30, 30, 30, 4, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142290758 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 Building ZINC001142290758 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142290758 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 988) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Cc2cccc(C(F)(F)F)c2)(NC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142290758.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142290758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001142290758 none CC(C)(C)OC(=O)N1CCC(Cc2cccc(C(F)(F)F)c2)(NC(=O)[C@@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 15, 10, 15, 10, 10, 10, 6, 10, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 10, 10, 10, 10, 19, 19, 30, 30, 30, 30, 4, 6, 6, 6, 10, 10, 10, 10] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 989) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,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(Cc2cccc(C(F)(F)F)c2)(NC(=O)[C@]([O-])([SiH3])c2ccco2)CC1) `ZINC001142290758.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142290758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001142290758 none CC(C)(C)OC(=O)N1CCC(Cc2cccc(C(F)(F)F)c2)(NC(=O)[C@]([O-])([SiH3])c2ccco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.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', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 11, 16, 11, 11, 11, 6, 10, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 4, 1, 4, 1, 1, 1, 6, 6, 6, 6, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 11, 11, 11, 20, 20, 30, 30, 30, 30, 4, 6, 6, 6, 11, 11, 11, 11] 50 rigid atoms, others: [25, 26, 27, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142290758 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142290758 Building ZINC001142291141 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142291141 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 990) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)c1ccccc1) `ZINC001142291141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001142291141 none Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 8, 12, 12, 30, 30, 30, 36, 36, 36, 36, 36, 36, 36, 21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 15, 15, 4, 8, 8, 8, 12, 12, 12, 12, 12] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 991) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)c1ccccc1) `ZINC001142291141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001142291141 none Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 41, 41, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 8, 13, 13, 38, 38, 38, 41, 41, 41, 41, 41, 41, 41, 25, 25, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 4, 8, 8, 8, 13, 13, 12, 13, 13] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142291141 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 Building ZINC001142291141 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142291141 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 990) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)c1ccccc1) `ZINC001142291141.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142291141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001142291141 none Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])c1ccco1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 36, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 12, 12, 8, 12, 12, 30, 30, 30, 36, 36, 36, 36, 36, 36, 36, 21, 21, 21, 21, 21, 21, 21, 21, 15, 15, 15, 15, 4, 8, 8, 8, 12, 12, 12, 12, 12] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 173 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 991) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)c1ccccc1) `ZINC001142291141.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142291141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 27 is the cov attach 4 27 0 4 27 1 4 27 2 3 27 2 30 to be deleted 31 to be deleted 32 to be deleted natoms 74 natoms 73 natoms 72 natoms 71 names: ZINC001142291141 none Cc1nnc(C(C)C)n1[C@@H]1C[C@H]2CC[C@@H](C1)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])c1ccco1)c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', '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', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 5, 5, 5, 8, 5, 7, 5, 5, 7, 5, 5, 5, 7, 5, 10, 5, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 41, 41, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 16, 16, 8, 4, 8, 4, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 8, 13, 13, 38, 38, 38, 41, 41, 41, 41, 41, 41, 41, 25, 25, 25, 25, 25, 25, 25, 25, 16, 16, 16, 16, 4, 8, 8, 8, 13, 13, 12, 13, 13] 50 rigid atoms, others: [25, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70]) total number of confs: 174 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142291141 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142291141 Building ZINC001142681967 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142681967 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 992) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cnc2c(c3cccc(C(F)(F)F)c3)c(C)nn2c1NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142681967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142681967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142681967 none CCOC(=O)c1cnc2c(c3cccc(C(F)(F)F)c3)c(C)nn2c1NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 15, 9, 9, 9, 9, 9, 9, 37, 37, 23, 37, 37, 37, 37, 37, 37, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 18, 18, 18, 18, 18, 9, 37, 37, 34, 37, 9, 9, 9, 9, 2, 2, 1, 2, 2] 50 rigid atoms, others: [26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 993) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cnc2c(c3cccc(C(F)(F)F)c3)c(C)nn2c1NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142681967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142681967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142681967 none CCOC(=O)c1cnc2c(c3cccc(C(F)(F)F)c3)c(C)nn2c1NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 17, 8, 17, 8, 8, 8, 8, 8, 8, 34, 34, 28, 34, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 19, 19, 19, 19, 19, 8, 34, 34, 34, 34, 8, 8, 8, 8, 2, 2, 1, 2, 2] 50 rigid atoms, others: [26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142681967 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 Building ZINC001142681967 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142681967 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 992) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cnc2c(c3cccc(C(F)(F)F)c3)c(C)nn2c1NC(=O)[C@@]([O-])([SiH3])c1ccccc1) `ZINC001142681967.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142681967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142681967 none CCOC(=O)c1cnc2c(c3cccc(C(F)(F)F)c3)c(C)nn2c1NC(=O)[C@@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 15, 9, 9, 9, 9, 9, 9, 37, 37, 23, 37, 37, 37, 37, 37, 37, 9, 9, 9, 9, 9, 6, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 18, 18, 18, 18, 18, 9, 37, 37, 34, 37, 9, 9, 9, 9, 2, 2, 1, 2, 2] 50 rigid atoms, others: [26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 993) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cnc2c(c3cccc(C(F)(F)F)c3)c(C)nn2c1NC(=O)[C@]([O-])([SiH3])c1ccccc1) `ZINC001142681967.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142681967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 28 is the cov attach 4 28 0 4 28 1 4 28 2 3 28 2 31 to be deleted 32 to be deleted 33 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001142681967 none CCOC(=O)c1cnc2c(c3cccc(C(F)(F)F)c3)c(C)nn2c1NC(=O)[C@]([O-])([SiH3])c1ccccc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'F', 'F', 'C.ar', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.2', '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'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1, 5, 8, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 17, 17, 8, 17, 8, 8, 8, 8, 8, 8, 34, 34, 28, 34, 34, 34, 34, 34, 34, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 2, 2, 1, 2, 2, 19, 19, 19, 19, 19, 8, 34, 34, 34, 34, 8, 8, 8, 8, 2, 2, 1, 2, 2] 50 rigid atoms, others: [26, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142681967 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142681967 Building ZINC001142682975 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142682975 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 994) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc(OC)c1OC) `ZINC001142682975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142682975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142682975 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 12, 12, 12, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 12, 12, 12, 14, 5, 7, 15, 14, 14, 14, 12, 5, 19, 19, 19, 38, 19, 5, 2, 2, 2, 1, 2, 2, 12, 14, 14, 14, 15, 15, 15] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 995) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc(OC)c1OC) `ZINC001142682975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142682975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142682975 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 10, 10, 10, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 13, 5, 5, 14, 12, 12, 12, 10, 5, 20, 20, 20, 40, 20, 5, 2, 2, 2, 2, 2, 2, 10, 13, 13, 13, 14, 14, 14] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142682975 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 Building ZINC001142682975 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142682975 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 994) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc(OC)c1OC) `ZINC001142682975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142682975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142682975 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [14, 12, 12, 12, 5, 5, 5, 5, 5, 19, 19, 19, 19, 19, 19, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 1, 2, 2, 12, 12, 12, 14, 5, 7, 15, 14, 14, 14, 12, 5, 19, 19, 19, 38, 19, 5, 2, 2, 2, 1, 2, 2, 12, 14, 14, 14, 15, 15, 15] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 995) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc(OC)c1OC) `ZINC001142682975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142682975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 21 is the cov attach 4 21 0 4 21 1 4 21 2 3 21 2 24 to be deleted 25 to be deleted 26 to be deleted natoms 63 natoms 62 natoms 61 natoms 60 names: ZINC001142682975 none COc1cc(c2cc(c3cccc(O)c3)cnc2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc(OC)c1OC 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', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 1, 1, 8, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 12, 5, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 4, 7, 7, 3, 7, 4, 9, 6, 8, 10, 11, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [12, 10, 10, 10, 5, 5, 5, 5, 5, 20, 20, 20, 20, 20, 20, 5, 5, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 10, 10, 10, 13, 5, 5, 14, 12, 12, 12, 10, 5, 20, 20, 20, 40, 20, 5, 2, 2, 2, 2, 2, 2, 10, 13, 13, 13, 14, 14, 14] 100 rigid atoms, others: [19, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142682975 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142682975 Building ZINC001142683527 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142683527 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 996) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c(Br)n2)c1) `ZINC001142683527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142683527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001142683527 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 34, 45, 34, 34, 34, 34, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 6, 6, 6, 34, 50, 50, 50, 50, 50, 34, 34, 34, 6, 6, 3, 3, 3, 1, 3, 3, 34] 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: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 997) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c(Br)n2)c1) `ZINC001142683527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142683527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001142683527 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 33, 33, 33, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 7, 7, 7, 33, 50, 50, 50, 50, 50, 33, 33, 33, 7, 7, 4, 3, 3, 1, 3, 3, 33] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142683527 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 Building ZINC001142683527 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142683527 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 996) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c(Br)n2)c1) `ZINC001142683527.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142683527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001142683527 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@@]([O-])([SiH3])c3ccccc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 34, 45, 34, 34, 34, 34, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 6, 6, 6, 34, 50, 50, 50, 50, 50, 34, 34, 34, 6, 6, 3, 3, 3, 1, 3, 3, 34] 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: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 997) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c(Br)n2)c1) `ZINC001142683527.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142683527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001142683527 none CCOC(=O)c1cccc(c2ccc(NC(=O)[C@]([O-])([SiH3])c3ccccc3)c(Br)n2)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', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 17, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 33, 43, 33, 33, 33, 33, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 3, 3, 1, 3, 3, 7, 7, 7, 33, 50, 50, 50, 50, 50, 33, 33, 33, 7, 7, 4, 3, 3, 1, 3, 3, 33] 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: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142683527 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142683527 Building ZINC001142684238 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142684238 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 998) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1) `ZINC001142684238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142684238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142684238 none COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 45, 18, 18, 10, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 45, 45, 18, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 1, 3, 3, 50, 50] 50 rigid atoms, others: [22, 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, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 196 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 999) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1) `ZINC001142684238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142684238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142684238 none COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 45, 17, 17, 10, 17, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 1, 3, 3, 50, 50] 50 rigid atoms, others: [22, 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, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142684238 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 Building ZINC001142684238 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001142684238 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 998) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1) `ZINC001142684238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142684238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142684238 none COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@@]([O-])([SiH3])c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 45, 18, 18, 10, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 45, 45, 18, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 1, 3, 3, 50, 50] 50 rigid atoms, others: [22, 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, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 196 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 mkdir: created directory `1' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/1 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 1 (index: 999) No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1) `ZINC001142684238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001142684238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 24 is the cov attach 4 24 0 4 24 1 4 24 2 3 24 2 27 to be deleted 28 to be deleted 29 to be deleted natoms 60 natoms 59 natoms 58 natoms 57 names: ZINC001142684238 none COc1ccc(CNC(=O)c2sc3nc(C)cc(C)c3c2NC(=O)[C@]([O-])([SiH3])c2ccccc2)cc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'S.3', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 8, 1, 11, 1, 14, 1, 8, 1, 5, 1, 1, 5, 1, 1, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 45, 17, 17, 10, 17, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 3, 3, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 45, 45, 17, 10, 10, 10, 10, 10, 10, 10, 3, 3, 3, 1, 3, 3, 50, 50] 50 rigid atoms, others: [22, 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, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 197 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142684238 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 1: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/1.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142684238 Building ZINC001142685978 mkdir: created directory `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142685978' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142685978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for ZINC001142685978 mkdir: created directory `0' /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142685978/0 /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142685978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Protomer 0 (index: 1000) grep: /scratch/xiaobo/281161/xco-8058088.67/working/3D/1000: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)c2cc(Cl)ccc21) `ZINC001142685978.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001142685978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142685978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001142685978 none CC(C)(C)OC(=O)N1CC2(CCN(C(=O)[C@@]([O-])([SiH3])c3ccccc3)CC2)c2cc(Cl)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', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 16, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 18, 28, 18, 18, 18, 18, 18, 6, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18] 50 rigid atoms, others: [48, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 52, 53, 54, 55, 56, 57, 58]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142685978 /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Finished preparing ZINC001142685978 Recording results /scratch/xiaobo/281161/xco-8058088.67/working /scratch/xiaobo/281161/xco-8058088.67 Appending to /scratch/xiaobo/281161/xco-8058088.67/finished/xco.* 0: /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142685978/0.* Removing working files in /scratch/xiaobo/281161/xco-8058088.67/working/building/ZINC001142685978 /scratch/xiaobo/281161/xco-8058088.67 Compressing combined databse files /scratch/xiaobo/281161/xco-8058088.67/finished/xco.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/281161/xco-8058088.67/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/913' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/656' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/935' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/770' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/586' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/690' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/653' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/704' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/670' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/906' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/377' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/775' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/536' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/945' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/668' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/635' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/535' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/967' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/831' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/938' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/603' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/550' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/622' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/416' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/528' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/460' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/436' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/970' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/748' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/840' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/647' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/852' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/965' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/735' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/890' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/365' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/925' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/801' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/665' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/728' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/447' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/820' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/520' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/751' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/518' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/826' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/974' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/960' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/885' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/402' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/758' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/805' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/813' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/993' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/994' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/555' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/830' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/617' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/688' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/481' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/355' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/806' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/552' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/345' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/963' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/357' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/443' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/710' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/509' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/545' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/391' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/538' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/437' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/880' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/917' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/337' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/825' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/367' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/918' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/671' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/413' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/897' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/595' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/614' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/995' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/983' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/450' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/341' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/492' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/568' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/827' 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`/scratch/xiaobo/281161/xco-8058088.67/working/3D/478' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/816' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/834' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/523' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/606' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/677' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/972' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/692' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/811' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/997' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/741' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/582' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/768' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/654' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/624' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/973' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/771' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/569' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/884' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/882' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/881' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/719' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/969' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/609' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/760' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/389' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/922' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/889' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/611' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/631' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/613' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/703' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/896' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/930' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/549' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/359' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/373' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/730' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/506' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/655' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/779' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/761' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/944' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/479' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/572' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/908' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/964' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/821' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/475' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/435' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/706' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/691' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/932' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/415' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/667' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/539' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/904' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/744' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/942' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/650' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/476' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/749' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/642' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/461' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/717' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/871' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/683' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/615' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/564' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/990' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/618' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/638' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/591' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/738' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/499' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/849' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/952' removed `/scratch/xiaobo/281161/xco-8058088.67/working/3D/421' 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`/scratch/xiaobo/281161/xco-8058088.67/working/protonate' -> `/scratch/xiaobo/281161/xco-8058088.67/archive' `/scratch/xiaobo/281161/xco-8058088.67/working/input-smiles.ism' -> `/scratch/xiaobo/281161/xco-8058088.67/archive/input-smiles.ism' rmdir: removing directory, `/scratch/xiaobo/281161/xco-8058088.67/working/building' rmdir: removing directory, `/scratch/xiaobo/281161/xco-8058088.67/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/logs `/scratch/xiaobo/281161/xco-8058088.67' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco' `/scratch/xiaobo/281161/xco-8058088.67/failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942/failure-reason' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/ZINC001180964942.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942/ZINC001180964942.ism' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/0.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942/0.failed' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/0.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942/0.failed/failure-reason' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/0.failed/0.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942/0.failed/0.mol2' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/0.failed/corina.trc' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942/0.failed/corina.trc' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942/input.ism' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/ZINC001180964942-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001180964942/ZINC001180964942-numbered.ism' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/failure-reason' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/0.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/0.failed' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/0.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/0.failed/failure-reason' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/0.failed/0.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/0.failed/0.mol2' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/0.failed/corina.trc' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/0.failed/corina.trc' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902.ism' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/input.ism' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902-numbered.ism' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902/failure-reason' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/0.failed' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902/0.failed' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/0.failed/failure-reason' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902/0.failed/failure-reason' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/0.failed/0.mol2' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902/0.failed/0.mol2' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/0.failed/corina.trc' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902/0.failed/corina.trc' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/ZINC001182894902.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902/ZINC001182894902.ism' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/input.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902/input.ism' `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/ZINC001182894902-numbered.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/failed/ZINC001182894902/ZINC001182894902/ZINC001182894902-numbered.ism' `/scratch/xiaobo/281161/xco-8058088.67/archive' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/archive' `/scratch/xiaobo/281161/xco-8058088.67/archive/xco-protonated-manual.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/archive/xco-protonated-manual.ism' `/scratch/xiaobo/281161/xco-8058088.67/archive/input-smiles.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/archive/input-smiles.ism' `/scratch/xiaobo/281161/xco-8058088.67/archive/xco-protomers.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/archive/xco-protomers.ism' `/scratch/xiaobo/281161/xco-8058088.67/archive/xco-protomers-expanded.ism' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/archive/xco-protomers-expanded.ism' `/scratch/xiaobo/281161/xco-8058088.67/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/finished' `/scratch/xiaobo/281161/xco-8058088.67/finished/xco.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xab/outputs/xco/finished/xco.db2.gz' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/failure-reason' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/ZINC001180964942.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/0.failed/failure-reason' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/0.failed/0.mol2' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/0.failed/corina.trc' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/0.failed' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/input.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942/ZINC001180964942-numbered.ism' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001180964942' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/failure-reason' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/0.failed/failure-reason' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/0.failed/0.mol2' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/0.failed/corina.trc' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/0.failed' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/input.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902-numbered.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/failure-reason' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/0.failed/failure-reason' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/0.failed/0.mol2' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/0.failed/corina.trc' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/0.failed' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/ZINC001182894902.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/input.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902/ZINC001182894902-numbered.ism' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902/ZINC001182894902' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/failed/ZINC001182894902' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/failed' removed `/scratch/xiaobo/281161/xco-8058088.67/archive/xco-protonated-manual.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/archive/input-smiles.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/archive/xco-protomers.ism' removed `/scratch/xiaobo/281161/xco-8058088.67/archive/xco-protomers-expanded.ism' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/archive' removed `/scratch/xiaobo/281161/xco-8058088.67/finished/xco.db2.gz' removed directory: `/scratch/xiaobo/281161/xco-8058088.67/finished' removed directory: `/scratch/xiaobo/281161/xco-8058088.67'